Mr O'Neill came under fire last week after an authorised book about his time at the White House, The Price of Loyalty, described Mr Bush as a disengaged figure lead by a "praetorian guard" of hardline rightwingers who were committed to invading Iraq from the beginning of his presidency.
Within hours of Mr O'Neill making his case in a televised interview on Monday evening the treasury department said its inspector general was investigating how a document marked secret was shown during the interview.
Mr O'Neill, who was sacked by Mr Bush in December 2002, insists that the documents were given to him by the treasury's legal officer in response to his request for any paperwork that would help the former Wall Street Journal reporter Ron Suskind write the book.
"I said to him [the legal officer] I would like to have the documents that are OK for me to have.
"About three weeks later the general counsel, the chief legal officer, sent me a couple of CDs, which I frankly never opened," he said.
Mr O'Neill says he sent the disks and documents to Mr Suskind, and that only the cover sheet shown on television bore the word secret.
Since he is the first insider to break rank with a White House that places a high premium on loyalty, the investigation is regarded as retribution for his outspoken criticism, although Mr O'Neill says that in the same position he would have done the same thing.
In the book, which has been damaging to Mr Bush's credibility, Mr O'Neill describes the often chaotic decision-making process at cabinet meetings, saying it made the president look "like a blind man in a room full of deaf people".
He says Mr Bush had his sights set on Saddam Hussein before the terrorist attacks of September 11.
"From the very beginning, there was a conviction that Saddam Hussein was a bad person and that he needed to go," Mr O'Neill told the CBS programme 60 Minutes.
He describes the reaction to the book as "red meat frenzy", and has tried to retract the more damaging quotes.
"It was not my intention to be personally critical of the president or anybody else," he says, but to cooperate with Suskind on a "chronicle of 23 months [in government]".
Of the "blind man quote" he said: "If I could take it back, I would take it back."
Pressed on whether he would vote for Mr Bush in November, he said he probably would, but that the American people needed to demand more of their leaders.
Mr O'Neill, a former aluminium mogul and longstanding Republican moderate, says the administration came to office determined to oust Saddam, and used the September 11 attacks as a convenient justification.
As Mr O'Neill, who sat in countless national security council meetings, describes the mood: "It was all about finding a way to do it. The president saying: 'Go find me a way to do this.'"
In the book, which is based largely on Mr O'Neill's recollections, the former treasury secretary says that as far back as January 2001, when President Bush took office, no one in the national security council questioned the assumption that Iraq should be invaded.