The Agriculture Department plans to warn consumers today that cooking pork in a microwave oven may not always destroy microorganisms that can cause trichinosis.

The findings resulted from an experiment designed to speed the process of cooking pork, and prompted the department to urge that a temperature of 170 degrees Fahrenheit be reached throughout the product in order to destroy any microorganisms that might be present.

Trichoinosis is rarely fatal. It usually results from eating insufficiently cooked pork from a pig infested with trichinae parasites. The disease is characterized by fever, nausea, diarrhea and muscular pains.

In 1979, 135 cases of trichinosis were reported, and the USDA estimates that there may be 150,000 to 300,000 cases of mild trichinosis in this country.

USDA's findings are similar to those of Dr. William J. Zimmermann of Iowa State University. In 1978, Zimmermann made the only previous study of how pork is affected if cooked according to directions given by mircrowave oven makers.

Until additional tests are completed this summer, it is not known whether the USDA has uncovered a serious health problem or an aberration.

At the USDA's Beltsville laboratory, pork containing trichinae was cooked by two methods.

". . . We found when we thawed frozen pork chops in a microwave oven and then cooked them in a charbroiler, [live] trichinae were observed in the digest from the cooked chops, and the trichinae were found [infective] when confirmed in rats," laboratory chief Anthony Kotula reported.

The laboratory also partiallyl cooked pork chops in a microwave oven, then finished them by deep fat frying. Live, but not infective, trichinae also were found in those chops.

Zimmermann said he believes the parasites were not killed because microwave ovens cook unevenly and leave "cold spots" in cooked meat.

In a study of microwave ovens in its March issue, Consumer Reports magazine said, ". . . Parts of the food may be heavily doused with energy. Other parts may receive very little. . . . Microwave ovens aren't renowned for cooking food evenly."

To compensate, some microwave manufacturers have installed platforms to revolve food. Others are using a fan-like apparatus to distribute microwave energy more evenly.