Congressional committees had asked for the papers to be submitted by Thursday.
This comes a day after the Senate demanded White House documents linked to its domestic spying programme.
Tensions with the White House have been building since Democrats took control of Congress in January and vowed to hold the administration to account.
Presidential counsel Fred Fielding said in a letter to the Senate and House of Representatives judiciary committees that he regretted no compromise had been found.
"We had hoped this matter could conclude with your committees receiving information in lieu of having to invoke executive privilege. Instead, we are at this conclusion," he wrote.
Mr Fielding said the administration had tried to co-operate with the investigation by releasing more than 8,500 pages of documents and sending some senior officials to testify.
But he said President George W Bush was not prepared to release documents revealing internal White House communications.
The row over the firing of eight federal US attorneys in 2006 has been building for several months.
Congress Democrats have been trying to force the resignation of Attorney General Alberto Gonzales, accusing him of firing the prosecutors for political reasons and then lying about the reason for their dismissal.
Some Republicans have also backed the moves.
But the president has dismissed the attempts to remove Mr Gonzales as themselves political.
White House officials say this is only the second time Mr Bush has invoked executive privilege.
The first was in December 2001, when Congress sought documents from the Clinton administration.