Tony Blair had said US-led teams have massive evidence that Saddam Hussein's regime had such facilities.
But in a pre-taped interview scheduled for transmission in London on Sunday, Bremer retreated when he learned that it was Blair who had made the claim.
Asked about the claim without being told first of the source, Bremer said: "I don't know where those words come from but that is not what (Iraq Survey Group chief) David Kay has said."
The US-led Iraq Survey Group is searching for weapons of mass destruction, one of the main justifications which Washington and London used to launch the March war.
But more than nine months into the occupation, no such weapons have been found.
"I have read (Kay's) reports so I don't know who said that," Bremer said in an interview on the British ITV1 channel with Jonathan Dimbleby.
"It sounds like a bit of a red herring to me," the American continued. "It sounds like someone who doesn't agree with the policy sets up a red herring then knocks it down."
Evidence made public
But Bremer retreated when told the claims were made by none other than President George Bush's staunchest ally Blair.
"There is actually a lot of evidence that had been made public," he said.
Blair claimed this month the Iraq Survey Group had found "massive evidence of a huge system of clandestine laboratories" in Iraq.
Bremer claimed the group had found "clear evidence of biological and chemical programmes".
"Weapons of mass destruction or no weapons of mass destruction, it's important to step back a little bit here, to see what we have done historically," he said.
In an interview with the British Forces Broadcasting Service on 16 December, Blair said: "The Iraq Survey Group has already found massive evidence of a huge system of clandestine laboratories, workings by scientists, plans to develop long-range ballistic missiles."
Blair did not go into detail, but a spokesman for the prime minister said that the findings were part of the interim report produced by the survey group several months ago.