Details of the claims emerged after the ex-agent filed a motion in a US federal court last week asking the US government to declassify legal documents which he said described a deliberate suppression of findings on Iran's nuclear programmes that ran against the CIA's view.
As a former undercover agent the man has been barred by the CIA from revealing his real name.
The motion follows a lawsuit the man filed in 2004 alleging the CIA had fired him after he questioned official CIA doctrine over both Iran and Iraq's nuclear programmes and argued with senior officials when attempting to file his reports contradicting assertions both nations were working on weapons programmes.
It also follows the release of an intelligence report last December as part of a US National Intelligence Estimate that concluded Iran had stopped work on nuclear weapons designs in 2003.
Western powers allege that Iran is attempting to build nuclear weapons, however Tehran says its programme is solely for peaceful purposes.
Assigned to undercover work in the Persian Gulf region, the ex-CIA agent, who is of Middle Eastern origin, recruited an informant who provided evidence that Iran had ended its research into designing and building a nuclear weapon, the man's lawyer, Roy Krieger, told the Washington Post.
However, when he tried to file a report on the findings his attempts were "thwarted" by CIA officials, the documents filed in court alleged.
Later two internal investigations were launched over the former operative's conduct, his lawyer said.
Krieger told the paper the investigations were a "pretext to discredit" the former operative and that the man was being punished by being forbidden by the CIA to reveal his name.
Paul Gimigliano, spokesman for the CIA, did not comment on the case specifically to the Washington Post but denied any allegation the CIA had suppressed reports.
"It would be wrong to suggest that agency managers direct their officers to falsify the intelligence they collect or to suppress it for political reasons," he told the paper.
"That's not our policy."