The White House has described media reports that it attempted to mislead the public over the destruction of CIA interrogation tapes as "pernicious".
The CIA is holding its own inquiry into the destruction of the tapes
Four senior administration lawyers, including former Attorney-General Alberto Gonzales, debated the fate of the tapes, the New York Times said.
The White House said the implication that it had hidden facts was "troubling" and should be corrected.
The Bush administration has refused to comment directly on the case.
The CIA's actions in destroying the tapes are currently the subject of three investigations.
Both the US justice department and Congress are probing exactly how and why the tapes came to be destroyed.
And the CIA itself is looking into the issue.
The Bush administration has so far refused to co-operate with the congressional investigation.
"We will continue to decline to comment on this issue, and in response to misleading press reports," press secretary Dana Perino said.
Nevertheless, she said: "The New York Times' inference that there is an effort to mislead in this matter is pernicious and troubling."
She added that the White House was formally seeking a change to the story - particularly the sub-headline, which read: "White House role was wider than it said."
The four lawyers the New York Times alleged were involved in the decision to destroy the tapes also included ex-White House counsel Harriet Miers.
Mr Gonzales served as White House counsel until 2005, until he was succeeded by Ms Miers.
The other two, according to the New York Times, were David Addington, a lawyer in Vice-President Dick Cheney's office, and John Bellinger, a national security council lawyer.
The newspaper said evidence suggested the involvement of White House officials in discussions about the tapes was more widespread than had previously been admitted.
Last week US Attorney General Michael Mukasey ruled that it was not appropriate for the White House to release information to Congress while the justice department was also probing the matter.
There has been speculation that the tapes, showing the interrogation of two al-Qaeda suspects, contained evidence of harsh treatment that critics say amounted to torture.
The CIA says it destroyed the tapes to protect the identity of its agents.