Over the past 12 years, John C. Beale was often away from his job as a high-level staffer at the Environmental Protection Agency. He cultivated an air of mystery and explained his lengthy absences by telling his bosses that he was doing top-secret work, including for the CIA.

For years, apparently, no one checked.

Now, Beale is charged with stealing nearly $900,000 from the EPA by receiving pay and bonuses he did not deserve. He faces up to three years in prison.

Beale, 64, who was a senior policy adviser in the Office of Air and Radiation, is expected to plead guilty at a hearing scheduled for Monday at U.S. District Court in Washington.

“This is a situation where one individual went to great lengths to deceive and defraud the U.S. government,” said EPA spokeswoman Alisha Johnson.

Beale’s attorney, John W. Kern, declined to comment on the case, as did a spokesman for U.S. Attorney Ronald C. Machen Jr.

At agency headquarters on Pennsylvania Avenue, Beale fostered an enigmatic image. He frequently traveled to China, South Africa and England, according to several people who worked with him. He would describe his trips and mention a lingering case of malaria.

The Arlington County resident told colleagues that his stints away from the office were for “sensitive work for another agency,” according to an official familiar with the situation who spoke on the condition of anonymity because the case is pending.

“I even asked him about it, as a joke,” said a person who knows Beale through work on environmental issues and spoke on condition of anonymity because of the pending charges. “We all actually believed that maybe there was something going on. He just kind of laughed it off.”

In recent weeks, people who work on environmental issues inside and outside the agency have learned of Beale’s alleged deceit and the matter has taken on some political weight.

Sen. David Vitter (La.), the top Republican on the Environment and Public Works Committee, called the alleged scheme a “massive fraud” and has demanded additional investigation by the inspector general to determine whether the alleged corruption extends further in the agency that protects the nation’s air, water and land.

Vitter said Beale had worked for Gina McCarthy, who now leads the EPA, for at least part of the time that he allegedly stole agency funds. The Louisiana Republican had threatened to filibuster McCarthy’s nomination to lead the agency over an unrelated matter.

McCarthy’s defenders said privately that she discovered the alleged activity and brought it to the attention of the authorities. She later forced Beale to retire in April 2013, according to a person familiar with the investigation. When he left, his base salary was $164,700.

Throughout the alleged scheme, which federal prosecutors said began in 2000, Beale appears to have acted alone, according to people close to the case.

The charges against Beale came in a three-page “criminal information,” which can only be filed with a defendant’s cooperation and signals that a plea agreement has been reached.

More details about how Beale carried out the alleged long-running scheme and exactly how much time he took off while still being paid are expected to emerge at his hearing before Magistrate Judge John M. Facciola.

Starting in about 2000, and continuing through Republican and Democratic administrations, court papers indicate that Beale was paid for work he never performed for the agency.

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 papers filed on Aug. 23.

The U.S. attorney’s office is seeking to recover $507,207 in a judgement against Beale. A separate restitution order for additional funds could be filed separately.

It is unclear whether Beale has the ability to repay the government. Property records show that Beale bought his 4,100-square-foot townhouse near Marymount University in 1996 for $536,000. His wife, Nancy Kete, is a managing director at the Rockefeller Foundation and previously worked for the EPA, according to her biography on the foundation’s Web site.

Phone messages left Wednesday for Beale and his wife were not returned. Beale, who has a master’s degree from Princeton University, began his career at the EPA in the late 1980s. He was intimately involved in the reauthorization of the Clean Air Act in 1990. During the George W. Bush administration, he coordinated the EPA’s discussions and activities on climate change with other agencies and the White House at a senior staff level.

Early on, his air-quality expertise led to many legitimate overseas trips and qualified him for annual bonuses, according to people familiar with the case.

“There was always an aura of mystery surrounding him,” said Frank O’Donnell, president of the environmental nonprofit Clean Air Watch, who was in various meetings with Beale. “He always projected confidence that he could fix any problem.”

Jennifer Jenkins contributed to this report.