WASHINGTON (AP) _ The nation's largest medical system, the Veterans Administration, is beset on two fronts with separate investigations into its physicians' licenses and the alleged coziness between employees and a drug company.

At least 49 VA doctors have been identified by the American Medical Association as having had their medical licenses revoked, suspended or restricted, officials of the AMA said Monday.

In a separate matter, the VA said between 75 and 100 employees accepted gifts, speaking fees and other favors from Smith Kline & French Laboratories, a Philadelphia company that sells pharmaceuticals to the VA medical system. All are employees of the VA's department of medicine and surgery.

Both investigations are being handled by the VA inspector general's office, which is charged by Congress as the agency's watchdog.

The finding on the doctors turned up when the AMA checked the names of physicians working for the VA in 1983 and 1984 against the AMA's listing of all licensed physicians.

It found 42 of 6,000 doctors working full-time for the VA and seven of 11,000 doctors working part-time for the VA during that period had license problems, said Dr. Richard L. Egan, director of the AMA's medical education division in Chicago.

But Dr. Arthur Lewis, deputy director for the VA's Office of Operations, denied unlicensed doctors might be working in VA facilities.

''I don't know at this point in time of any individual serving in a VA hospital who does not have a valid license in some state,'' Lewis said.

In some cases the doctors may have multiple licenses and retained a license in at least one state, Egan said.

The licenses may have been lost due to medical competence problems, or for other reasons. In most states conviction of a felony is grounds for revocation, and doctors may have lost their licenses because of tax convictions or other charges not directly related to medicine, Egan said.

''I think one has to consider that these problems range not only over time but over significance,'' said Egan. ''We would then leave to the VA to follow up on what we can report from our files.''

In some cases the doctors may no longer be working for the VA, and there was some confusion at the agency over just how many doctors are invovled.

While the AMA said it has given the 49 names to the VA, Dr. Arthur Lewis, deputy director for the VA's Office of Operations, said the VA has received about 40 names in all, including 12 from the AMA in preliminary findings. Others have come from state boards of medicine and other sources, he said.

Lewis said they appeared to involve doctors who still had valid licenses somewhere.

Spokeswoman Donna St. John said a VA auditor was going to AMA headquarters in Chicago to see the latest findings.

AMA officials said they are now checking another 77,000 doctors associated with the VA as residents, consulting and attending physicians, and doctors who do patient work on a fee or voucher basis for the VA.

Lewis is heading a committee to review the findings.

Ms. St. John said in cases ''that appear to be serious and might pose a threat to patient care ... the physician will be suspended pending individual review.''

In the Smith Kline case, Ms. St. John said the inspector general's office had determined that VA employees accepted favors that included meals, entertainment, theater tickets, other gifts and unreported speaking fees.

She refused to say how much money was involved.

''Some of these amounts are modest. Some are substantial,'' she said.

Smith Kline spokesman Alan Wachter said his company has cooperated with the VA investigation for more than a year. He said Smith Kline's actions had been ''consistent with traditional practices and applicable law.''

Ms. St. John said the VA intends to impose penalties ranging from dismissal to suspension and formal admonishments. In minor cases, she said, the only action may be counseling for the employee.

The VA refused to disclose any employee names or to describe the jobs of those involved. All are employees of the VA's department of medicine and surgery.

U.S. Medicine, a newspaper for government physicians, said that as a result of the investigation, some personnel have been removed from hospital formulary committees, which determine what drug products are bought.

The VA operates 172 medical centers, 103 nursing units and 226 outpatient clinics around the country, and has a medical budget of more than $9 billion.