American protein crystallization experiments will be carried aboard the Soviet Union's permanently manned space station MIR under an agreement between a Massachusetts company and the Soviet government, officials said yesterday.

The pact between Payload Systems Inc. of Wellesley, Mass., and the Soviet Union has been under negotiation for nearly a year, according to company officials. They said Payload Systems represents clients, including pharmaceutical companies, that do not want to be identified but want to perform the research on MIR.

Officials of the Commerce and Defense departments said they recently gave routine approval for export of the experiments, which are expected to be launched beginning next year.

Once before, in the mid-1980s, the Defense Department gave approval for an American scientific experiment to be flown aboard a Soviet craft. That case involved a study of Halley's Comet, a Defense spokesman said. The Payload Systems experiments presented no technology transfer concerns and were approved under a "routine technical data licensing application," the spokesman said.

An administration official familiar with the experiments said their approval for export does not indicate any loosening of federal opposition to the launching of American-made communications satellites on Soviet rockets, which he said would present considerable national security concerns about the transfer of technology.

The Soviet Union has given considerable emphasis to materials research that takes advantage of the weightlessness of space. The United States currently lacks a facility that stays in orbit long enough to perform such experiments.

Payload Systems Inc., a consulting firm, was founded in 1984 by scientist Byron K. Lichtenberg. In 1983, while with the Massachusetts Institute of Technology, he became the first nonastronaut American to fly on the space shuttle.