The Pentagon has a backlog of more than 600,000 employees awaiting investigations for security clearances in part because a $100 million effort to computerize the process has been a massive failure, government officials and members of Congress said yesterday.

The new computer system installed by the Defense Security Service, which conducts the background checks, has "not operated as intended, is not year 2000 compliant and may cost about an additional $100 million to stabilize," according to a report this month by the General Accounting Office, an investigative arm of Congress.

New background investigations, which are supposed to take 90 days, on average are taking 204 days, the GAO said. Based on a representative sample, it appears that less than 1 percent of the investigations are completed within the 90-day time frame, and almost 10 percent take more than a year, the report said.

"This is a huge, massive failure," a senior staff member of the Senate Armed Services Committee said yesterday. He added, however, that committee members believe the Pentagon has begun to remedy the situation by appointing retired Air Force Lt. Gen. Charles J. Cunningham Jr. to head the 2,500-person Defense Security Service.

Cunningham was named to the post on Nov. 8, just five days after the GAO report was made public. He succeeds Steven T. Schanzer, who had headed the security service for 19 months and had been its chief operating officer since 1997.

Assistant Defense Secretary Arthur L. Money also has promised to follow some of the GAO's recommendations, including an immediate "Y2K testing and mitigation" program to ensure that the $100 million computer system, installed in October 1998, will not confuse the year 2000 with the year 1900.

The Defense Security Service receives requests for first-time security checks on about 120,000 people a year. It also conducts periodic reinvestigations of personnel who already hold security clearances. Such reinvestigations are overdue on more than 600,000 employees of the Defense Department and private contracting firms.

As a result of this backlog, "hundreds of thousands of individuals can access classified information without assurances of their trustworthiness and reliability," the GAO concluded.

About 2.4 million military, civilian and contractor employees hold security clearances. Of that total, roughly 524,000 have "top secret" clearances that require reinvestigation every five years. About 1.8 million have "secret" clearances that are supposed to be reviewed every 10 years, and fewer than 100,000 have "confidential" clearances that require renewal every 15 years.

The GAO report attributes the backlog to a dramatic drop in the number of field investigations that occurred when the Pentagon cut back its old system of handling cases "before assuring that the new computer system worked."

Even if the new computer system is made operational, the GAO warned, the Defense Department "may have to replace it in order to meet user requirements."

As of August, the Defense Security Service, with the assistance of the Air Force, had been unable to determine exactly what would be needed to solve the computer system's various hardware and software problems, and estimates of the cost ranged from $100 million to more than $300 million, the report said.

In the meantime, the GAO suggested that the Pentagon identify high-priority security investigations and provide funds to ensure that they are carried out "in a timely manner."

The GAO report was requested by Rep. Ike Skelton (Mo.), the ranking Democrat on the House Armed Services Committee, who called its findings "very serious." But the release of the report this month was accompanied by little publicity or reaction on Capitol Hill.

That treatment came in sharp contrast to the congressional uproar earlier this year over security lapses and allegations of Chinese espionage at the Energy Department's nuclear laboratories. Four congressional committees held hearings on the national laboratories, the Energy Department appointed a new "security czar," and Congress created a semi-autonomous agency to oversee the facilities that design and build nuclear weapons.

Since 1982, 68 military and civilian employees of the Defense Department and 12 workers at private defense contractors have been convicted of committing espionage. They include such high-profile spies as former Navy communications expert John A. Walker Jr., who gave secrets to Moscow, and Navy intelligence analyst Jonathan Jay Pollard, who provided top-secret material to Israel.

In addition, "hundreds of other potential instances have been detected," the GAO said, but no convictions were obtained because "individuals defected or committed suicide or the cases were settled in other ways."