A virulent mystery disease has claimed five whooping cranes at the Patuxent Wildlife Research Center in Laurel, a loss that reduces the total population of the endangered birds in North America to fewer than 160, officials said yesterday.

Preliminary tests indicate the unusual deaths may have been caused by a microorganism, said Dr. Jim Carpenter, research veterinarian for the U.S. Fish and Wildlife Service's captive propagation program at the center.

He said scientists at the fish and wildlife service's National Wildlife Health Laboratory in Madison, Wis., found signs of a microorganism in tissue studies of the dead birds, although they do not know yet what it is. "They might have the best handle to date," he said, "but we won't know for sure for weeks."

In the meantime there is heavy security at the 4,700-acre refuge at Patuxent, the largest wildlife research center in the world, where the 34 remaining captive whoopers are in quarantine and under close scientific surveillance. Only one handler is allowed into their pens, and he washes his shoes before entering each of the outdoor cubicles for fear of carrying the disease, Carpenter said.

The first of the whoopers died Sept. 17, after appearing healthy the night before, Carpenter said. That pattern was repeated as grown, seemingly healthy birds were found dead Sept. 24 and 26 and Oct. 25.

When a 2-year-old female fell ill Sunday afternoon, Carpenter said, he and his chief assistant spent the next six hours administering antibiotics and fluids, but the bird died anyway.

Carpenter said if a microorganism is to blame, it may have been carried by a wild, injured bird that was brought into the center last spring. "We're checking that bird for antibodies now," he said.

Another possibility is that the organism has been harbored by the captive whoopers for years and a mutant, virulent form of it developed suddenly.

Besides the tissue studies at the Madison lab, Carpenter said samples are being analyzed for toxins at the National Veterinary Services Lab in Ames, Iowa, and for bacteria at the National Zoo in the District and at Maryland's Animal Health Lab in Salisbury. All other tests have been negative, he said.

Only once before in the 17 years the Patuxent center has been studying whoopers and raising chicks for release into the wild has disease struck so earnestly. In 1978-79, sickness took three chicks and one adult whooper and six sandhill cranes, which serve as "foster parents" for whooper chicks in the wild. The organism causing those deaths has not turned up in investigation of the latest outbreak.

While he regards the loss of the five birds as "very significant," Carpenter said some mortality is inevitable with captive flocks. "We're all disappointed, but we can't tell what the long-term significance is until we know what the disease is. I expect we'll identify it, figure out a control and come out stronger for it in the end."

There are two flocks of wild whooping cranes left in North America, one of 90 birds currently migrating between Canada and Texas, and a second flock of about 35 birds that is migrating from Idaho to a refuge in New Mexico.