For the first time, the federal government has punished a scientist for violating federal rules governing genetic engineering research.

In a report released yesterday by the National Institutes of Health, Ian Kennedy, formerly of the University of California at San Diego, was cited for carrying out gene experiments with a virus that was outlawed for experimentation under guidelines in effect at the time, and for failing to seek the required permission to carry out a second series of experiments with the same virus.

The NIH action will, in effect, stop Kennedy from getting NIH funds for two years. An NIH official said that the danger of the experiment was small, but that the government took the action to assert the importance of the federal rules in protecting against serious hazards that might arise out of genetic engineering experiments.

Kennedy has maintained that the incident was an accident. He says he got permission for, and intended to experiment with, a less harmful virus. Kennedy resigned his position with bitter comments last fall when the university issued a report saying his work with the more dangerous virus may have been intentional, although it stopped short of calling Kennedy's story untrue.

NIH director Donald Frederickson ordered a copy of the NIH report be attached to any NIH grant application filed by Kennedy in the next two years, thus making it less likely the application would be approved. If Kennedy did not get a grant to do genetic engineering experiments in the next two years, Frederickson said, his work may be subject to special conditions or additional scrutiny.

"The greatest punishment in this case was already levied by Kennedy on himself, when he resigned from the university," said Bernard Talbot, executive secretary of the Recombinant DNA Committee, which investigated the incident for the NIH. "He can't get an NIH grant if he's not at a university. If he was still at the university, we probably would have taken stronger action against his ongoing grants."

Yesterday's NIH report avoided the issue of whether Kennedy intentionally or accidentally worked with the more dangerous virus. The report said that even without resolving that question, there was proof of a serious violation of the federal rules and evidence that "responsible scientific practice" was not followed.

The incident began in January 1980, when four graduate students in Kennedy's laboratory reported to the department chairman their suspicions that he was working with a virus called the Semliki Forest virus, rather than the Sindbis virus, with which he had permission to work.

Both viruses cause ill effects in humans -- including fever and skin rash -- but the Semliki virus was once reported to have killed a person.

Scientists have acknowledged the possibility that dangerous hybrids may be formed in the experiments, thus the federal guidelines. The genetic engineering techniques extract one or more genes from an organism, in this case the Semliki virus, and implant the genes in another organism. In principle, the effect of the new genes on the new host organism cannot be known before the experiment, so it is possible the organism may gain new, dangerous properties.

Ironically, the experiment conducted by Kennedy is now allowed under the federal rules. At the time, however, the rules disallowed any experiments with the genetic material of the Semliki and other dangerous viruses. The stringent safety conditions now required to work with the Semliki virus are the same one Kennedy used during his experiments.

Kennedy has said the batches of the two viruses -- Semliki and Sindbis -- were mixed up by someone outside his laboratory who entered the lab to "sabotage" his work. Kennedy did insert the Semliki genes into another organism, they multiplied, and Kennedy used the new organism in a series of experiments.

The NIH said it would be useless to try to determine the truth of the switch of viruses. But Kennedy never sought or received permission to use new organisms with Sindbis or Semliki genes. Thus, his experiments following grounds for his punishment.

Kennedy is now out of work and is reportedly seeking a position in a commercial firm to continue his research.