The Food and Drug Administration is trying to protect some people who don't want to be protected -- prisoners who volunteer as guinea pigs for drug research.

In a new rule published in the Federal Register, the FDA has in effect halted use of prisoners in drug and other medical research. The agency says it will not accept any findings for drug marketing based on such tests. The FDA rule is similar to an earlier one from the former Department of Health, Education and Welfare that barred use of federal funds in conducting such research.

The strongest opposition to the proposed rule under consideration for two years came from prisoners who received money for participating in drug testing.

The issue arose in 1976 when the use of prisoners for medical testing was widespread and essentially unregulated by government. An American Civil Liberties Union lawsuit uncovered questionable activities, particularly at a prison in Jessup, Md. These included injecting prisoners with disease virus such as malaria to test new drugs.

The ACLU lawsuit led to a national study in 1977 that looked into weather prisoners were being coerced into taking part in the research. The study determined that the "overriding motivation" for prisoner participation was money.

But the study went on to say that because the participants were in prison, money was more influential in getting their consent, and thus they were "more readily available for the imposition of burdens which others would not willingly bear."

HEW and FDA in 1978 recommended that all research using prisoners be halted except for health problems of people who were incarcerated.

During the rule-making period, FDA received only 40 comments on the proposed ban. The most critical were from drug companies which said the controlled life and diet for prisoners is important for drug studies. But forceful and objections also came from prisoners and prison groups. They complained that, in addtion to the incentive of money, prison volunteers believe their participation represented a way of repaying society for the crimes that had commmitted.

But the FDA has ruled the wall become final next June 1, and the interim the few studies now under way will have to be concluded.

Drug companies, one FDA official said, have begun advertising on college campuses for students to take over as human guinea pigs.