In this Sept. 18, 2013 file photo, EPA administrator Gina McCarthy testifies on Capitol Hill. (Cliff Owen/Associated Press)

A human resources official for the Environmental Protection Agency became aware as early as 2008 of “problems” with a high-ranking official who pleaded guilty last year to scamming the agency out of $900,000, according to documents released Tuesday by Sen. David Vitter (R-La.).

Scott Monroe, director of human resources in the EPA’s Office of Air and Radiation, who approved John C. Beale’s time cards, told investigators that he checked into Beale’s failure to come to work and was told that Beale worked for the CIA and that he had malaria, neither of which proved to be true, according to a summary of the interview.

In 2010, Monroe began pressing to cancel large, undeserved bonuses that Beale had been receiving and was scheduled to continue getting. The bonuses pushed Beale’s pay over a statutory limit.

“John Beale has been receiving a retention bonus of 25% every year since 1991. EPA policy requires that OAR recertify the bonus annually and re-establish the bonus every three years,” Monroe wrote on Jan. 12, 2011, in a note to Gina McCarthy, who was chief of OAR at the time and now heads the EPA. “EPA has no records to show that these recertifications occurred except for one in 2000,” said the note Vitter’s office released.

Retention bonuses are paid to valued employees whom the agency risks losing to the private sector, which usually can offer better pay. The investigation of Beale’s activities has shown that Robert Brenner, a close friend who recruited him to the EPA, repeatedly recommended Beale for the bonuses.

But McCarthy told the investigators for the inspector general’s office that when she turned to Craig E. Hooks, head of the Office of Administration and Resource Management, five days later, he told her not to pursue the case because it was a criminal matter.

“McCarthy relied on Craig Hooks for advice on how to handle the situation but was advised by Hooks to ‘stand down’ on the matter since it was a criminal matter, and that Hooks would refer to the [inspector general],” said a summary of the investigators’ interview with McCarthy in November.

Those comments could help explain a 25-month lag before McCarthy took action against Beale — a delay that was noted in the inspector general’s December report. But Hooks, in the second of two interviews with the investigators, denied telling McCarthy that the Beale case was a criminal matter.

“Craig asserts that he never told Gina McCarthy that the John Beale matter was a criminal matter,” the investigator wrote in a summary released by Vitter. Hooks did, however, mention it to Inspector General Arthur A. Elkins, the documents show.

Attempts to reach Hooks at his home and office and by e-mail were unsuccessful. An aide said he was out of the country on vacation. Monroe, who was reached at home Monday night, declined to comment.

The documents provide the fullest picture of how the long-running fraud Beale committed was allowed to continue even after suspicions about him surfaced. Beale was sentenced in December to 32 months in prison for taking pay and about $500,000 in bonuses he did not deserve while he posed as a CIA officer.

Vitter, Rep. Darrell Issa (Calif.) and other Republicans have been critical of management lapses that allowed Beale to continue collecting pay and bonuses and run up large travel expenses. The inspector general’s office, some EPA officials and Democrats have credited McCarthy with finally questioning Beale’s fiction and forcing him to retire.

The e-mails were part of a memo critical of McCarthy that Vitter released Tuesday to GOP members of the Senate Environment and Public Works Committee, on which he is the ranking Republican.

No action was taken against Beale for two years — until January 2013, when McCarthy ordered him to return to work full time, and February, when she canceled his retention bonuses. By then, McCarthy and other high-ranking officials had attended Beale’s retirement party, although he continued working and receiving his pay.

In both interviews, Hooks told investigators that an unusual document in Beale’s file made him presume that Beale actually was a CIA officer. He also said in one that he had difficulty gathering all the facts, in part because Beale was not coming to work.

In response to questions from an investigator, Hooks said that when Beale announced his retirement, there was no longer a need to determine whether he worked for the CIA. Shown an e-mail McCarthy wrote on April 2, 2012, saying that she had taken no action against Beale on his advice, Hooks said he considered this a matter of national security and wanted to “err on the side of caution,” according to the investigators’ summary.

Alice Crites contributed to this report.