Investigators said 60-year-old Richard Macias logged in 168 times to look at celebrity applications, sometimes even printing them out.
Federal prosecutors charged Macias on Wednesday with three misdemeanor counts of exceeding authorized computer access.
Authorities said Macias worked for the passport agency for 24 years, most recently as a fraud prevention manager.
Macias told the San Francisco Chronicle that he only looked at people's applications in order to do his job. He also said he plans to plead guilty in the case.
The names of the celebrities involved have not been released.
The Associated Press contributed to this report.