The records relate to Bush's service in the Air National Guard three decades ago and are likely to help in throwing light on the president's whereabouts while he was a pilot during the Vietnam war.
In an election year, Bush is facing strident accusations of having dodging military duty in his youth.
Defence Finance and Accounting Service spokesman Bryan Hubbard said the microfilm payroll records were found in Denver and blamed a clerical error for the Pentagon's failure to find the records.
"We are talking about a manual process for records that are over 30 years old," Hubbard said.
The Pentagon earlier this month said microfilm records of large numbers of service members, including Bush, were ruined in 1996 and 1997 in a project to save large, brittle rolls of microfilm.
Bush claims to have moved to Alabama in May 1972 to perform his guard service there for a year.
But other guard officers have said they had no recollection of seeing him there.
Last February, the White House released hundreds of pages of Bush's military records. Those records did not provide new evidence to place Bush in Alabama during the latter part of 1972 – the period Democrats say he was basically absent without leave.