The Bush administration took office amid heavy criticism of Mr. Clinton’s last-minute pardons, most notably to Marc Rich, the fugitive financier whose ex-wife had donated to Mr. Clinton’s presidential library.

Image Michael Milken, the former junk bond king turned philanthropist, as he left Federal Court in Manhattan in April 1989. Credit... Keith Meyers/The New York Times

Against that backdrop, Mr. Bush has made little use of his clemency powers, granting just 157 pardons and six commutations. By comparison, over eight years in office President Ronald Reagan granted clemency 409 times and Mr. Clinton 459 times. More than half of Mr. Clinton’s grants came in his final three months.

Fred F. Fielding, the White House counsel, declined to be interviewed about clemency plans.

Erik Ablin, a Justice Department spokesman, said the administration was committed to “giving each clemency petition received the careful review that is necessary to make an appropriate recommendation.” Mr. Ablin noted that any cases left unresolved by Mr. Bush would stay open for his successor.

As the administration wrestles with the cascade of petitions, some lawyers and law professors are raising a related question: Will Mr. Bush grant pre-emptive pardons to officials involved in controversial counterterrorism programs?

Such a pardon would reduce the risk that a future administration might undertake a criminal investigation of operatives or policy makers involved in programs that administration lawyers have said were legal but that critics say violated laws regarding torture and surveillance.

Some legal analysts said Mr. Bush might be reluctant to issue such pardons because they could be construed as an implicit admission of guilt. But several members of the conservative legal community in Washington said in interviews that they hoped Mr. Bush would issue such pardons  whether or not anyone made a specific request for one. They said people who carried out the president’s orders should not be exposed even to the risk of an investigation and expensive legal bills.

“The president should pre-empt any long-term investigations,” said Victoria Toensing, who was a Justice Department counterterrorism official in the Reagan administration. “If we don’t protect these people who are proceeding in good faith, no one will ever take chances.”