WASHINGTON — A government watchdog testified Thursday there may have been problems with a security clearance background check conducted on the 29-year-old federal contractor who disclosed previously secret National Security Agency programs for collecting phone records and Internet data.

Appearing at a Senate hearing, Patrick McFarland, the U.S. Office of Personnel Management’s inspector general, said USIS, the company that conducted the background investigation of former NSA systems analyst Edward Snowden, is now under investigation.

McFarland declined to say what triggered the inquiry of USIS or whether the probe is related to Snowden. But when asked by Sen. Jon Tester, D-Mont., if there were any concerns about the USIS background check on Snowden, McFarland answered: “Yes, we do believe that there may be some problems.”

USIS, based in Falls Church, Va., has offices in Grove City and Boyers.

McFarland declined after the Senate hearing to describe to reporters the type of investigation his office is conducting. Sen. Claire McCaskill, D-Mo., said she was told the inquiry is a criminal investigation related “to USIS’ systemic failure to adequately conduct investigations under its contract.”

“We are limited in what we can say about this investigation because it is an ongoing criminal matter,” said McCaskill, chairwoman of the Senate subcommittee on financial and contracting oversight. “But it is a reminder that background investigations can have real consequences for our national security.”

McCaskill’s panel conducted the hearing jointly with Tester’s subcommittee on efficiency and effectiveness of federal programs.

USIS said in a statement that it has never been told that it is under criminal investigation. USIS received a subpoena from the inspector general’s office in January 2012 for records, the statement said. “USIS complied with that subpoena and has cooperated fully with the government’s civil investigative efforts,” according to the company.

USIS declined to comment on whether it conducted a background investigation of Snowden. The company said it performs thousands of background investigations each year for OPM and other government agencies. “These investigations are confidential and USIS does not comment on them,” the USIS statement said.

The background check USIS did on Snowden was done in 2011 and was part of periodic reinvestigations that are required for employees who hold security clearances, according to McFarland and Michelle Schmitz, the assistant inspector general for investigations at OPM.

Booz Allen Hamilton, the company where Snowden was working at the time of the disclosures, fired him for violations of the firm’s code of ethics and firm policy.