An American who has been missing in Iran for more than six years was secretly working for the CIA and not on a private business trip as the US government has long claimed. Robert Levinson, a former FBI agent, disappeared in March 2007 after flying to Kish Island, an Iranian resort known as a haven for smugglers and mobsters. An Associated Press (AP) investigation has now disclosed that Mr Levinson had been hired by a rogue group of CIA analysts, who dispatched him to gather intelligence without permission from their superiors. The US government has for years maintained the cover story that the 65-year-old Mr Levinson was a private citizen, while behind closed doors the spy agency was rocked by his disappearance. The CIA reportedly paid his family $2.5 million (£1.54m) to prevent a lawsuit that would reveals its role and launched an internal crackdown against the analysts who were managing him. Three of them were sacked while another seven faced disciplinary action, the AP reported. The news agency said it had delayed publishing details of Mr Levinson’s links with the CIA three times because the US government said it was closing in on leads to bring him home. Mr Levinson’s whereabouts remain unclear and some believe he is dead while others suspect he is being secretly held at the behest of the Iranian government. If he remains alive he will have been held captive longer than any other missing American, including the journalist Terry Anderson who was imprisoned by Hezbollah for 2,454 days. The White House condemned AP’s decision to publish the story and said Mr Levinson was "not a government employee when he made that trip". But it refused to comment on his reported links to the CIA. “The White House and others in the US Government strongly urged the AP not to run this story out of concern for Mr Levinson’s life,” said Caitlin Hayden, a spokeswoman for the National Security Council. “We regret that the AP would choose to run a story that does nothing to further the cause of bringing him home.” John Kerry, the US secretary of state, also declined to comment during a diplomatic trip to Israel. There has been no trace of Mr Levinson since April 2011, when his family was sent a photograph of him dressed in a Guantánamo Bay-style jumpsuit. In the five photographs, the shackled American is seen holding signs reading: “Why can you not help me?” The Iranian government initially claimed that Mr Levinson had been arrested but since then has denied any knowledge of his whereabouts. The White House has come under fire for not demanding the return of Mr Levinson, and two other Americans being held in Iran, as part of the recent nuclear deal agreed in Geneva.