John Beale, 64, who was a senior policy adviser with the EPA's Office of Air and Radiation is expected to plead guilty during a hearing Monday at the U.S. District Court in Washington, The Washington Post reported.
He is accused of stealing the money by fraudulently claiming pay and bonuses he didn't deserve, the agency said.
"This is a situation where one individual went to great lengths to deceive and defraud the U.S. government," EPA spokeswoman Alisha Johnson said.
Beale's attorney, John W. Kern, and a spokesman for U.S. Attorney Ronald C. Machen Jr. declined to comment to the Post on the case.
Starting in about 2000, Beale was paid for work he never performed for the agency, court papers alleged. He apparently acted alone.
He received a salary, benefits and "retention incentive" bonuses "for which Beale had not earned by providing employment services to the EPA," Assistant U.S. Attorney James E. Smith said in the court documents filed last month.
Sen. David Vitter, R-La., the top Republican on the Environment and Public Works Committee, called the scheme a "massive fraud" and demanded further investigation to determine the extent of the alleged corruption.
Vitter said Beale had worked for Gina McCarthy, the current EPA chief, for at least part of the time he allegedly stole agency funds.
McCarthy's supporters said she discovered the alleged activity and alerted authorities. She also forced Beale to retire in April 2013, a person familiar with the investigation told the Post.
The Post said the U.S. attorney's office seeks to recover $507,207 in a judgment against Beale. A separate restitution order for more money also could be filed.