Monday's announcement of the probe comes less than 24 hours after O'Neill sharply criticised President George Bush on the CBS programme 60 Minutes.
O'Neill, who resigned a year ago in a shake-up of Bush's economy team, said on the programme that he had seen no "real evidence" during his two years in the administration that Iraq had weapons of mass destruction.
He said Bush had been intent on ousting Saddam Hussein since well before the attacks of 11 September 2001, and he described the president's management style as disinterested and unengaged.
In his first public response, Bush brushed aside O'Neill's comments on Monday, telling a news conference in Mexico that "like the previous administration, we were for regime change" in Iraq.
Giving a joint news conference with President Vicente Fox in Monterrey where they were attending a regional summit, he avoided a direct answer on whether he felt betrayed by O'Neill.
"We're asking them to simply look into the '60 Minutes' segment and then take appropriate steps, if necessary."
US Treasury spokesman
Nor did he address the fact that the weapons of mass destruction that the war was fought over had never been found.
"Now he (Saddam) is no longer in power and the world is better for it," Bush said.
White House spokesman Scott McClellan said O'Neill's criticism "appears to be more about trying to justify personal views and opinions than it does about looking at the results that we are achieving."
IG office to investigate
Treasury spokesman Rob Nichols told reporters the department had asked its Inspector General's office to investigate how a document marked "secret" had come to be shown during the "60 Minutes" interview with O'Neill.
"We're asking them to simply look into the '60 Minutes' segment and then take appropriate steps, if necessary," he said, adding that the legal threshold for asking for an inquiry was "very low."
Asked if the Treasury risked being seen as vindictive in seeking the probe, Nichols said, "We don't view it in that way."
The Bush administration has previously been accused of acting vindictively towards a critic of its invasion of Iraq - former ambassador Joseph Wilson.
Last year Wilson accused administration officials of compromising his wife's safety by leaking the fact that she was an undercover agent for the CIA in retaliation for his criticism.
O'Neill called Bush a "blind man
in room full of deaf men"
A spokesman for "60 Minutes" said the programme had not been given access to any secret documents.
'No secret papers'
"We have no secret documents. We merely showed a cover sheet that eluded to... a secret document," the spokesman said, describing the secret document as dealing with a post-Saddam Iraq.
The programme was aired in conjunction with publication of a book based on O'Neill's experiences in the Bush administration, "The Price of Loyalty," written by journalist Ron Suskind.
Suskind, who also appeared on "60 Minutes", said O'Neill had given him access to thousands of administration documents.
In the book the former Treasury Secretary, the first major Bush administration insider to attack the president, described Bush during Cabinet meetings as being like "a blind man in a room full of deaf people".
The book was likely to provide fodder for attacks on Bush from Democratic presidential candidates who have accused him of using faulty intelligence on the extent of Iraq's weapons programme as a pretext for war.
O'Neill could not immediately be reached for comment on the Treasury probe request.