- NEW: Source: The CIA apologized to the family, paid $2.5 million settlement
- NEW: Family: "It is time for the U.S. government to step up"
- AP and Washington Post: Bob Levinson was working for the CIA in Iran
- Officials and family have previously denied government ties to the trip
(CNN) -- A former FBI agent who went missing in Iran was working for the CIA there, not conducting private business as officials have previously claimed, The Associated Press and the Washington Post reported on Thursday.
Both the State Department and Bob Levinson's family have long denied he was working for the U.S. government when he disappeared on a trip to Iran in 2007.
But Thursday's reports from the Washington Post and the AP claim that Levinson had been on a CIA mission to dig up information.
A source who's involved in the matter told CNN that there's proof that Levinson worked for the CIA undercover and under contract while also working as a private investigator.
WH calls for Levinson release 
Longest-held American hostage 
U.S. tourist and Korean War veteran Merrill Newman arrives at the Beijing airport Saturday, December 7, after being released by North Korea. Newman was detained October 26 by North Korean authorities just minutes before he was to depart the country after visiting through an organized tour. His son Jeff Newman says the Palo Alto, California, man had all the proper paperwork and set up his trip through a North Korean-approved travel agency. 
An Iranian court threw out a death penalty conviction last year for Amir Hekmati, a former U.S. Marine charged with spying. But he still remains in solitary confinement at Iran's notorious Evin Prison. Hekmati was detained in August 2011 during a visit to see his grandmother; his family and the Obama administration deny accusations that he was spying for the CIA. 
A North Korean court sentenced Kenneth Bae, a U.S. citizen, to 15 years of hard labor for committing "hostile acts" against the state. Those alleged acts were not detailed by the country's state-run news agency when it announced the sentence Thursday, May 2. Bae, here in a photo from a Facebook page titled Remember Ken Bae, was arrested in November. "This was somebody who was a tour operator, who has been there in the past and has a visa to go to the North," a senior U.S. official told CNN. 
Mexican authorities arrested Yanira Maldonado, a U.S. citizen, right, on May 22, for alleged drug possession. She and her husband, Gary, were traveling from Mexico back to the United States when their bus was stopped and searched. She was released on Friday, May 31 and is back in the United States. 
Saeed Abedini, a 33-year-old U.S. citizen of Iranian birth, was sentenced to eight years in prison in January, accused of attempting to undermine the Iranian government and endangering national security by establishing home churches. 
North Korea has arrested Americans before, only to release them after a visit by a prominent dignitary. Journalists Laura Ling, center, and Euna Lee, to her right, spent 140 days in captivity after being charged with illegal entry to conduct a smear campaign. They were freed in 2009 after a trip by former President Bill Clinton. 
Former President Jimmy Carter negotiated the release of Aijalon Gomes, who was detained in 2010 after crossing into North Korea illegally from China. Analysts say high-level visits give Pyongyang a propaganda boost and a way to save face when it releases a prisoner. 
Eddie Yong Su Jun was released by North Korea a month after he was detained in April 2011. His alleged crime was not provided to the media. The American delegation that secured his freedom included Robert King, the U.S. special envoy for North Korean human rights issues. 
Robert Park was released by North Korea in 2010 without any apparent U.S. intervention. The Christian missionary crossed into North Korea from China, carrying a letter asking Kim Jong Il to free political prisoners and resign. North Korea's state-run news agency said Park was released after an "admission and sincere repentance of his wrongdoings." Here, Park holds a photo of Kim and a malnourished child during a protest in Seoul. 
Josh Fattal, center, Sarah Shourd, left, and Shane Bauer were detained by Iran while hiking near the Iraq-Iran border in July 2009. Iran charged them with illegal entry and espionage. Shourd was released on bail for medical reasons in September 2010; she never returned to face her charges. Bauer and Fattal were convicted in August 2011, but the next month they were released on bail and had their sentences commuted. 
Haleh Esfandiari, an Iranian-American scholar, was also detained at Evin Prison, spending months in solitary confinement before Iran released her on bail in August 2007. Esfandiari was visiting her ailing mother in Tehran when she was arrested and charged with harming Iran's national security. 
Alan Gross, at right with Rabbi Arthur Schneier, has been in Cuban custody since December 2009, when he was jailed while working as a subcontractor. Cuban authorities say Gross tried to set up illegal Internet connections on the island. Gross says he was just trying to help connect the Jewish community to the Internet. Former President Jimmy Carter and New Mexico Gov. Bill Richardson have both traveled to Cuba on Gross' behalf, but they were unable to secure his release. 
Sixteen Americans were among the dozens arrested in December 2011 when Egypt raided the offices of 10 nongovernmental organizations that it said received illegal foreign financing and were operating without a public license. Many of the employees posted bail and left the country after a travel ban was lifted a few months later. Robert Becker, right, chose to stay and stand trial. 
Freelance reporter James Foley went missing in November after his car was stopped by gunmen in Syria. He is likely being held by the Syrian government, according to the GlobalPost, an online international news outlet to which he contributed, and Foley's brother. 
Filmmaker Timothy Tracy was arrested in Venezuela in April on allegations of funding opponents of newly elected President Nicolas Maduro, successor to the late Hugo Chavez. Tracy went to Venezuela to make a documentary about the political division gripping the country. 
Retired FBI agent Robert Levinson has been missing since 2007. His family says he was working as a private investigator in Iran when he disappeared. It's believed Levinson, now 64, is being held captive somewhere in southwest Asia. 
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Americans detained abroad The AP says it decided to move forward with publishing the sensitive story after holding off several times.
"The AP first confirmed Levinson's CIA ties in 2010 and continued reporting to uncover more details. It agreed three times to delay publishing the story because the U.S. government said it was pursuing promising leads to get him home," the news agency said in its report. "The AP is reporting the story now because, nearly seven years after his disappearance, those efforts have repeatedly come up empty. The government has not received any sign of life in nearly three years. Top U.S. officials, meanwhile, say his captors almost certainly already know about his CIA association."
CNN's source, who declined to be identified because of the sensitive nature of the investigation, said that after six and half years in captivity and interrogations, it's more than likely that Levinson's captors know he was working undercover.
"The family is aware of the risk created by this story and are praying for his safety, as they have for six years," a Levinson family spokesman told CNN Thursday night. "All they want is to bring Bob home."
In a written statement, the family criticized the U.S. government's response to the situation.
"Bob is a courageous man who has dedicated himself, including risking his own life, in service to the U.S. government. But the U.S. government has failed to make saving this good man's life the priority it should be. There are those in the U.S. government who have done their duty in their efforts to find Bob, but there are those who have not," the statement said. "It is time for the U.S. government to step up and take care of one of its own. After nearly 7 years, our family should not be struggling to get through each day without this wonderful, caring, man that we love so much."
Officials contacted by CNN on Thursday declined to comment on any alleged ties between Levinson and the U.S. government.
"We have no comment on any purported affiliation between Mr. Levinson and the U.S. Government," CIA spokesman Chris White said. "The U.S. Government remains committed to bringing him home safely to his family."
National Security Council spokeswoman Caitlin Hayden criticized the AP for publishing the story and said it "does nothing to further the cause of bringing him home."
"Without commenting on any purported affiliation between Mr. Levinson and the U.S. government, the White House and others in the U.S. Government strongly urged the AP not to run this story out of concern for Mr. Levinson's life," she said. "We regret that the AP would choose to run a story that does nothing to further the cause of bringing him home. The investigation into Mr. Levinson's disappearance continues, and we all remain committed to finding him and bringing him home safely to his family."
AP: 'One of the biggest scandals in recent CIA history'
The agent-turned-security-consultant was last heard from on March 8, 2007, when he checked into a hotel on Iran's Kish Island and then checked out to return to the United States the next day.
From the start, the CIA and the State Department denied there were any government ties to Levinson's trip.
And Levinson's family said he had been in Iran on private business investigating cigarette smuggling.
But the Washington Post and AP reports differ sharply from public government descriptions.
After Levinson's disappearance, the Washington Post and AP reported, CIA officials initially downplayed his ties with the agency and said he did not go to Iran for the agency.
"But months after Levinson's abduction, e-mails and other documents surfaced that suggested he had gone to Iran at the direction of certain CIA analysts who had no authority to run operations overseas," the Washington Post story says, citing officials. "That revelation prompted a major internal investigation that had wide-ranging repercussions at Langley."
The AP's story describes the situation as "one of the biggest scandals in recent CIA history."
According to the reports, the CIA changed how analysts work with contractors as a result. And the agency paid $2.5 million to Levinson's family, the Washington Post and AP said.
Source: CIA apologized to family
CNN's source said that David McGee, a family friend who used to be a federal prosecutor in Florida, helped find the documents that proved Levinson's CIA connection. Ever since Levinson's disappearance, McGee had been trying to do whatever he could to locate his friend.
With the help of his paralegal, McGee found e-mails exchanged between a CIA analyst and Levinson. The e-mails discussed Levinson's 2007 trip to Iran, the source said. And more importantly, they revealed the trip had a CIA connection, as the AP and the Washington Post reported.
McGee took the e-mails to the Senate Intelligence Committee and to Sen. Bill Nelson from Levinson's home state of Florida, a committee member at the time, the source said.
At first, the source said, the CIA denied any involvement.
"As a result of the documents, they conducted an investigation and discovered it was true," the source said.
A CIA representative asked to meet Levinson's family in Pensacola, Florida, the source said, and "personally apologized on behalf of the CIA."
McGee met with the CIA and negotiated a $2.5 million settlement with Levinson's family to fend off a lawsuit, the source told CNN.
But all the while, in public statements, the U.S. government continued to deny any ties between Levinson and the CIA -- work that, according to the AP and Washington Post reports, was done off the books.
As a results of the investigation, three CIA employees were fired and seven others were disciplined, the source said.
At least two of the three people fired have been rehired by other government agencies, a source told CNN, confirming information first reported by the AP.
"They fired their own people and then took care of them," the source said.
The Justice Department opened a criminal investigation into the matter, according to the source. So far, the source said, no one has been charged.
Justice Department spokesman Andrew Ames declined to comment.
Where is Levinson?
Levinson's whereabouts remain unclear.
During an exclusive interview with CNN's Christiane Amanpour in September, Iranian President Hassan Rouhani offered little when asked what he could tell Levinson's family.
"We don't know where he is, who he is," Rouhani said. "He is an American who has disappeared. We have no news of him."
In 2011, the State Department said new evidence suggested that Levinson, who has diabetes and high blood pressure, was alive and being held somewhere in southwest Asia.
This year, a source with knowledge of the investigation told CNN, "we have every reason to believe that he's alive and that the Iranians control his fate."
Last month, Levinson became the longest held American hostage in history.
At the time, Levinson's family members told CNN's New Day that they were worried because they haven't had any word since they received five photos in 2011.
The pictures show Levinson in an orange jumpsuit, holding messages.
"We have not received any recent information about him," said his wife, Christine Levinson, "although I do believe he is safe and will come home to us soon."
Wife of U.S. pastor held in Iran pleads for his freedom
CNN's Jim Sciutto and Tori Blase contributed to this report.
