Mr. Gates made clear that most troubling was that the inquiry showed how little the Air Force had done to improve the security of the nuclear weapons infrastructure even after it was disclosed last year that a B-52 bomber had flown across the United States without anyone’s realizing that it was carrying six armed nuclear cruise missiles.

Mr. Gates, whose military service includes a year as an intelligence officer within the Air Force’s nuclear program, emphasized that neither incident posed a danger of a nuclear mishap.

Nevertheless, he said, the inquiry made it clear that the Air Force had suffered for years from a loss of expertise in handling nuclear materials. He acknowledged that the Air Force had taken steps to improve the situation, but he said that more must be done to fix “structural, procedural and cultural problems.”

Mr. Gates, 64, served as deputy national security adviser and director of central intelligence under the first President George Bush. He has repeatedly said that he plans to retire from government service at the end of the Bush administration, but there has been speculation that he may be asked to stay on by either a President McCain or a President Obama after January, to help guide the Pentagon while the country is at war.

Pentagon officials said General Moseley, in his role as a member of the Joint Chiefs, met Thursday with Adm. Mike Mullen, the chairman, who supported the decisions for both officials to retire.

The errors in handling nuclear weapons components constituted more than just an indication that the cold-war-era focus on these powerful weapons had become fuzzy. They have also put the Bush administration in a difficult position, as the United States is struggling to prevent nuclear technology from spreading to nations that do not have it and has criticized North Korea and Iran for their nuclear ambitions. American officials have even spoken strongly to Russia for not sufficiently safeguarding its stockpile.