Aaron Alexis, the Navy Yard shooter who had received secret-level security clearance for his work for the military, was one of roughly 2 million individuals whose backgrounds are scrutinized annually by the Office of Personnel Management, which handles security checks for more than 100 federal agencies.

As it has coped with the massive volume of checks, the agency has struggled to maintain consistent investigative standards, according to independent oversight officials, who have repeatedly urged OPM to improve the quality of its security checks.

Since 2007, 21 investigators and record checkers who work on security clearances for OPM have been convicted of or pleaded guilty to falsifying their reports by recording fake answers to questions and claiming to have done record checks that never occurred, among other actions. The staff and contractors involved compromised the integrity of at least 240 security checks for federal applicants and current employees, including 203 top-secret clearance investigations, according to the OPM’s office of inspector general.

“There is an alarmingly insufficient level of oversight of the Federal Investigative Services program,” Patrick McFarland, the agency’s inspector general, said at a Senate hearing in June. “The lack of independent verification of the organization that conducts these important background investigations is a clear threat to national security.”

McFarland said he believes there may be “considerably more” fraud in the investigative process. “I don’t believe we’ve caught it all by any stretch,” he said.

Separately, the Government Accountability Office has documented gaping holes in OPM’s investigative files. In May 2009, the GAO found that 87 percent of about 3,500 investigative reports the Defense Department used in security clearance decisions were missing required documentation. It urged the office to better measure how often its reports met federal investigative standards.

OPM has yet to take that step, Brenda Farrell, the GAO’s director of defense capabilities and management, said in an interview.

“We have been on record for some time that there is a need for performance measures for these investigative files to help manage and oversee what is going on,” she said. “We have had discussions, we’ve asked for documentation and we have not seen any evidence they have done that.”

OPM officials did not immediately respond to requests for comment Tuesday. But in his testimony at the June Senate hearing, Merton Miller, associate director of investigations for OPM’s Federal Investigative Services, defended his agency’s work.

“We have no backlogs, are meeting timeliness mandates and have increased automation,” Miller said.

“We’ve got quality procedures in our contracts for our contractors, as well as our federal employees, where there are several stages and several layers of review that occur when a background investigation is being worked and when it is finalized,” he added.

Miller said missing pieces of information in case files were sometimes the result of a lack of cooperation by an applicant’s past employers or an inability to interview subjects because they were deployed abroad.

The role the agency played in Alexis’s security clearance probably will intensify the spotlight on OPM, already under sharp scrutiny from lawmakers in the wake of former National Security Agency contractor Edward Snowden’s disclosure of classified material.

More than 4.9 million federal government workers and contractors held a security clearance in 2012 — the vast majority of whom work for the Defense Department, according to the Office of the Director of National Intelligence, which is responsible for developing government-wide policies on background investigations.

The bulk of the federal government’s security clearance checks is conducted by OPM’s Federal Investigative Services, which relies on a network of 2,500 federal employees and 6,700 contractors to do the investigations. (Some national security and law enforcement agencies— such as NSA, the Central Intelligence Agency and the Federal Bureau of Investigations — handle background investigations internally, rather than rely on OPM.)

The office relies on “federal investigative standards” and “internal guidance” as the criteria for what information to collect, according to the GAO.

The workload is enormous. In fiscal year 2011, OPM received more than $1 billion to conduct more than 2 million background checks, according to the GAO. The cost of each investigation varies widely, depending on how deep investigators dig into the background of an applicant. In 2012, the base price for a top-secret clearance investigation conducted by OPM was $4,005, while the base price of a secret-level clearance investigation was $260, according to the GAO.

The office passes along its finding to the federal agencies that requested the checks, which then determine whether an applicant merits clearance.

In the case of Alexis, the Defense Department had to sign off on his security clearance after it was conducted by OPM.

It is unclear why the Department of Defense signed off on Alexis’s original 2007 background check after his 2004 arrest in Seattle for shooting out the tires of a car, and why his clearance was not revoked after his more recent brushes with the law, which included a disorderly conduct arrest in DeKalb County, Ga., in 2008, and a 2010 gun incident in Texas.

Thomas Richards, a spokesman for the Office of Personnel Management, said the only security clearance review his office conducted of Alexis occurred in 2007. That investigation turned up his 2004 arrest in Seattle.

A Pentagon spokesman said the Department of Navy Central Adjudication Facility determined in March 2008 that Alexis was eligible for access to secret information. Such lower-level clearances are typically good for 10 years, and can be extended to former military personnel who become contractors.

“According to applicable federal investigative standards, an individual with Mr. Alexis’ non-critical level of eligibility would only need to be reinvestigated once every ten years,” the official said. “In the absence of unadjudicated derogatory information and/or a break-in employment greater than 24 months, contractors may be reciprocally granted eligibility and access based on an existing eligibility.”

The Experts, the Fort Lauderdale, Fla., company that employed Alexis in the last year, twice confirmed his security clearance with the Defense Department, the company said Tuesday.

“The latest background check and security clearance confirmation were in late June of 2013 and revealed no issues other than one minor traffic violation,” the company said in a statement.

Thomas Hoshko, chief executive of The Experts, told The Washington Post that he would not have hired Alexis had he known about his past arrests.

“Anything that suggests criminal problems or mental health issues, that would be a flag,” he said. “We would not have hired him.”

A security check for secret-level clearance is far less intensive than one for top-secret clearance. It requires a check of the FBI database, military records and data from law enforcement agencies where an applicant has lived, worked and attended school during the past five years. It does not require interviews with family members, co-workers or employers.

Marjorie Censer, Alice Crites, Tom Hamburger ,Carol Leonnig and Craig Whitlock contributed to this report.