The FBI is running a check on 41,000 federal employes who work in computer and benefit payment programs at the Department of Health and Human Services to determine if they have ever been convicted of felonies.

The computer check of police and court records nationwide was initiated after the department issued a report last month on the criminal activities of 46 federal workers, state employes and contractors who worked for the government on HHS benefits programs. They had been caught authorizing excessive payments or issuing bogus checks to themselves or friends.

The department noted that 18 percent had previous criminal records -- often for similar crimes -- but had not disclosed them on their job application forms, as required by law.

Many of the HHS employes now being checked are assigned to the Social Security Administration headquarters in Baltimore and the department's benefits offices here. They make up about a third of the department's work force.

Criminal convictions do not necessarily disqualify applicants from federal employment. But, depending on the crime, convictions can preclude assignment to jobs that involve money, some computer functions, national security or benefits programs. Under federal policy, an employe who has been convicted of embezzlement, for instance, would be barred from handling funds.

The records check was initiated by the agency's inspector general to determine the suitability of workers whose jobs involve authorizing or processing benefits. HHS benefits include the Social Security, Medicare, Medicaid and family assistance payments that go to about one in six Americans.

HHS sent the FBI computer tapes containing 41,000 employe names last month to determine if those workers concealed criminal records when they applied to the government or if they have been convicted of felonies since coming to work.

An HHS official said that in some cases employes with criminal records may be transferred to other jobs even if the convictions are listed on their applications. Where convictions are not listed, employes could be fired, he said.

Another HHS official who asked not to be identified said that at other agencies where in-house computer fraud or benefit abuse has been discovered, similar FBI name checks are being considered. But spokesmen for several government agencies denied it yesterday.

In the official notice of the record check program, published in the May 8 issue of the Federal Register, HHS officials pledged that any FBI data sent to the department would be closely guarded by its inspector general's office. Tapes will be burned or shredded after the investigation is completed, HHS said.

Last month's report on criminal activity was an update of a 1982 survey of 172 computer-related fraud and abuse cases during the previous five years, about half of which involved federal employes. The latest report contained interviews with federal workers convicted during that period.

Typically, they were nonsupervisory personnel in their 30s who earned $20,000 a year or less (the average federal salary in the Washington area is about $31,000). About half were caught by coworkers or supervisors within six months. The typical "loss" was $45,000, but about one in five defrauded the government of $100,000 or more before being caught, HHS said.

Some of the workers interviewed said they had opened bank accounts in the names of Social Security recipients who had recently died, and then cashed their checks. Others authorized illegal, or excessive, payments to confederates with whom they split the money, or in some cases created beneficiaries and cashed their checks.

Several officials of federal unions said yesterday they had not heard about the computer checks.