The chief of research at the Environmental Protection Agency violated agency rules when he appeared to help a longtime business associate secure a $77,000 research contract that the agency already had rejected, EPA's inspector general has concluded.

Andrew P. Jovanovich, EPA's acting assistant administrator for research and development, was placed on leave with pay four months ago pending the outcome of the investigation.

Jovanovich, who was handpicked for the $50,000-a-year job last summer by EPA Administrator Anne M. Gorsuch, insisted he has done nothing improper. He called the inspector general's report "30 pages of rather unpleasant innuendo."

Jovanovich said EPA's research division is in disarray and that some allegations were coming from "career bureaucrats whose empires would be disrupted by the changes I was making . . . . They Gorsuch's office should either charge me with something or end the investigation."

The Jovanovich flap is the latest in a series of management upheavals for Gorsuch. Enforcement counsel William A. Sullivan Jr. resigned this week, while James W. Sanderson, Gorsuch's choice for the agency's No. 3 job, has been waiting since January for the inspector general to complete a conflict-of-interest investigation into actions he took as a consultant to EPA. Sanderson has denied any conflict.

In a related development, a study released yesterday by Sen. Max Baucus (D-Mont.) found that EPA's research division has a poor track record in monitoring consulting contracts worth millions of dollars. The General Accounting Office study said that a third of the contracts it reviewed in detail were of little or no value to EPA. The GAO study covered contracts awarded in 1979 and 1980, but it said many of them are still in place today.

In Jovanovich's case, an internal report by inspector general Matthew N. Novick concluded that he violated EPA regulations because his "actions . . . gave a strong appearance of preferential treatment."

Rep. Toby Moffett (D-Conn.) wrote Gorsuch this week to ask why she had taken no action more than a month after receiving the report. "How much longer is the EPA going to continue to employ a high official who has been found by the agency's inspector general to have attempted to award contracts on the basis of friendship instead of merit?" he asked. An EPA spokesman would say only that Gorsuch has made no decision yet.

The controversy began last summer when Jovanovich received a visit from Ronald Probstein, an engineering professor at the Massachusetts Institute of Technology, whom he has known for years. Probstein said in an interview that he angrily complained that his proposal to study waste-water treatment technology had been rejected by an EPA peer review panel, and that this would force him to lay off several graduate students. Probstein said this week he just wanted "another chance" to proceed with important research. Andrew P. Jovanovich, the research chief, said some allegations came from "career bureaucrats whose empires would be disrupted by the changes I was making."

"He was very angry when they turned him down," Jovanovich said in an interview. "I said I'd see what I could do to help."

Jovanovich said he asked the EPA grants office to find other peer reviewers to reconsider Probstein's project. An EPA grants official told investigators that Jovanovich's office recommended one scientist and told him to ask Probstein to recommend another one. Probstein did and the two scientists went on to praise the proposal. Jovanovich's division then awarded MIT $77,223 for the project.

Jovanovich said this week that he had only a friendly business relationship with Probstein, and that he highly valued Probstein's previous work, which Jovanovich supervised when he worked for a private research institute in Denver before joining EPA. Jovanovich said that EPA's grants officials "are very poor at selecting the right work" and that he saw no problem with an applicant suggesting someone to review his work.

But the inspector general said that "allowing a scientist to select his own peer reviewer, especially one he has previously worked with, lacks any appearance of independence or objectivity . . . and would leave EPA open to charges of cronyism."

The inspector general is still investigating a related allegation that Jovanovich "pressured" an EPA official into adding $55,000 to an existing contract with a consulting firm that Probstein partially owns. Jovanovich dismissed the charge as unfounded.

The inspector general also examined Jovanovich's actions last August, when, according to the report, Jovanovich's office contacted MIT officials and suggested they hire Warren Muir, a career EPA manager who was about to leave the agency, to do some additional work on the Probstein project. That same month, Jovanovich said, he temporarily stayed at Muir's house in Virginia while looking for a place to live.

After Muir left EPA, Jovanovich signed an amendment to the MIT contract, providing another $20,200 to hire Muir. When other EPA officials failed to approve the arrangement, the report said, MIT nevertheless charged Muir's work to the agency as part of Probstein's contract. Jovanovich said he saw nothing wrong with paying for Muir's work right after he left EPA because "he was very familiar with the research of the agency."

Muir could not be reached for comment. The inspector general said he had been concerned initially about the appearance of favoritism in the Muir case, but that the agency's general counsel concluded that no agency regulation had been violated. EPA canceled both contracts when the inspector general's investigation began.

The GAO study, meanwhile, looked at 444 consulting contracts, mainly in the research division, and found that many of them were of questionable value. EPA repeatedly modified 256 of these contracts, which increased their cost by 150 percent, or $191 million, GAO said.

Since the start of the Reagan administration, the auditors said, EPA has continued to hire consulting firms for basic regulatory work--such as writing pollution regulations, inspecting factories and classifying toxic chemicals--that should be done by EPA's own employes. But these contracts also are being scaled back as the agency's research and enforcement budgets have been cut by a third.