Government investigators reported Thursday that a controversial Food and Drug Administration official thinks like the meat producers whose $40 billion-a-year industry he regulates.

But they said they "found no evidence whatever of any corrupt or dishonorable conduct" on the part of Dr. C. D. Van Houweling, director of the Bureau of Veterinary Medicine since 1967.

The Department of Health, Education, and Welfare ordered the investigation after 11 subpoenaed FDA employees - eight from the BVM, three from the agency's Bureau of Foods - testified under oath in January, 1975, before two Senate subcommittees headed by Sen. Edward M. Kennedy (D-Mass.).

They generally alleged that Van Houweling ran the BVM in an autocratic way that discouraged dissenters, particularly those who favored more vigorous regulation of the use of medicines and chemicals that possibly could leave trace residues in livestock and poultry products for human consumption.

The staff members also alleged that BVM approved animal drugs not proved to be safe and effective, was relaxed about traces of cancer-causing agents in food-producing animals, and delayed - sometimes for years - regulatory action that a good manager would have taken.

HEW referred the allegations to its Review Panel on New Drug Regulation, a special group of seven lawyers and scientists headed by New York University Law Prof. Norman Dorsen. The panel assigned the investigation to special counsel Frank E. Schwelb, who wrote a 420-report, Thursday, the panel sent the report to Health, Education and Welfare Secretary Joseph A. Califano Jr. with a letter expressing its "general agreement" with Schwelb's conclusions and recommendations.

Schwelb said his investigation of Van Houweling and his senior aides "confirmed a general producer orientation and a comparatively lenient view towards residue problems."

He cited an interview in which the BVM chief said that "we put the economic benefit to the producer into the benefit-to-risk ratio. If the drug is available to everyone, then food is produced more cheaply, and the consumer benefits."

Schwelb also cited an interview in which former FDA cousel Peter Barton Hutt said that Van Houweling is "not prejudiced for industry, but rather for the viewpoint shared by industry . . . His honest personal viewpoint coincides with industry. He's no in industry's pocket."

Hutt and others who frequently clashed with Van Houweling stoutly defended his integrity and good faith. To weave him into a conspiracy theory "could not be more wrong," Hutt said.

Van Houweling emphatically denied to Schwelb that he had taken reprisals against staff critics of his policies, saying his intention was to preserve what he considered to be a scientific atmosphere.

"We are satisfied of his sincerity," Schwelb wrote.Nonetheless, some staff members "are reluctant to speak their minds for fear of reprisal," even if the record "does not support any allegation of vindictiveness, or even of any heartless indifference to people's feelings."

And Schwelb documented Van Houweling's assertion that he had taken a tough regulatory stance against industry to halt or try to halt sales of several animal drugs for which the evidence of safety and effectiveness was inadequate.

The report established that Van Houweling had dealt with critical memos - including some about what he thought were innocuous traces of a cancer-causing chemical in turkey rolls - by "suppression."

Schwelb, faulting Van Houweling's "management style," said that the substitution of suppression for debate is "inappropriate and impermissible."