A special government investigative panel says that top Food and Drug Administration officials harassed and humiliated 12 FDA medical officers and outside advisers during the Nixon and Ford administrations so as "to make the agency less adversarial" toward the pharmaceutical industry.

The new leaders of the Department of Health, Education, and Welfare and the FDA should apologize and make other amends to the scientists, the panel said.

It is said that HEW and the EDA, perceiving the scientists as anti-industry, has tried to "neutralize" them through exile to various EDA Siberias and through other improper and sometimes illegal conduct. Generally, the scientists insisted to the panel that rather than being anti-industry, they were obeying the law that drugs must be proved safe and effective.

The panel - seven lawyers and scientists appointed by HEW - disclosed that it had referred to the Justice Department evidence of possible criminal conduct by Dr. Henry E. Simmons, director of the FDA's Bureau of Drugs from April, 1970, to August, 1973. The department decided, however, that it did not have a viable case.

The evidence concerned possible perjury, cover-up of material facts, obstruction justice, and conspiracy to obstruct justice, all in connection with an unsuccessful administrative grievance proceeding initiated by Dr. John O. Nestor, one of the 12 FDA scientists.

The panel also urged the new FDA commissioner, Donald Kennedy, to invite Simmons' successor, Dr. J. Richard Crout, and Dr. Marion Finkel , chief of new-drug evaluation, to show cause why they should not be reprimanded, partly for misleading the hearing examiner in Dr. Nestor's grievance hearing.

The Review Panel on New Drug Regulation, as it is called, adopted the conclusions and recommendations made by its special counsel, Frank E. Schwelb, in a 766-page report scheduled for release today. A reporter obtained a copy yesterday.

Schwelb's report "represents a rare occasion on which allegations made by federal employees against the management of their agency have been thoroughly investigated by an impartial body and the resuits of that investigation made public," panel chairman Norman Dorsen, a New York University law professor, said in a transmittal letter to HEW Secretary Joseph A. Califano Jr.

Califano, in a memo randum last night to Kennedy and acting Assistant Secretary for Health James F. Dickson, said he is "determined to eliminate any question of irregular procedures or improper influence in the decisions of FDA."

He pledged to give the report "painstaking review and prompt follow-up where appropriate," and directed the officials to let him know by May 31 whether apologies and reprimands are justified.

The investigation was rooted in hearings at which 40 FDA scientists - subpoenaed and under oath - testified before the Senate Health and Administrative Practice and Procedure Subcommittes, starting in August, 1974.

Last night, the chairman of the subcommittees, Sen. Edward M. Kennedy (D-Mass.), termed the report " a serious indictment" and said the new FDA commissioner must make sure that agency scientists are never again subjected to scuh "unprofessional and indefensible actions."

Schwelb and his staff speak in their report of an "atmosphere of paranoia and hostility" in FDA during the years in question. They tell a story of demoralization caused by higher-ups who failed to level with subordinates, foul-ups and mismanagement, byzantine maneuverings and back-stabbings, and some dedication and courage as well.

Their report said that during the last two administrations FDA was "not . . . dominated by the pharmaceutical industry," and "often took a firm regulatory posture, although individual cases of inappropriate contacts with drug companies occurred."

But starting in 1970, when Dr. Charles Edwards headed the FDA, the agency began "a conscious effort" to be "more cooperative with drug manufacturers" mainly because of an opinion that scientists, particularly in the unit responsible for cardiovascular drugs, were holding back valuable medicines.

The panel, named by HEW Secretary Casper W. Weinberger after the first Senate hearings in 1974, agreed with Schwelb that sometimes unlawful involuntary transfers used to "neutralize" medical officers and others were patterned after a manual devised by Alan May, an HEW official in the Nixon era. A federal grand jury here indicted May last Jan. 14 for allegedly conspiring to deny civil servants the chance to compete for career jobs without political discrimination.

While nominating Crout and Finkel for possible reprimands, Schwelb did so with "great reluctance," saying that both were outstanding scientists who had made important contributions and had willingly cooperated in the investigation.

Schwelb also said that the two doctors felt they had a severe problem with some of their in-house critics, particularly Dr. Nestor, because of what they perceived as the critics' personal abrasiveness, disruptiveness and anti-industry bias.

At the same time, Schwelb said, Simmons, Crout and other administrators treated the critics with "unlawfulness, dishonesty, discourtesy, lack of consideration and even apparent vindictiveness."

The report said Crout acknowledged shabby treatment of child psychiatrist Carol Kennedy, described by several witnesses as "a crusader for children's safety," and others, including consultant Gerald Solomons.