(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.
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.
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."
CNN's Jim Sciutto and Tori Blase contributed to this report.