An independent commission of lawyers and pathologists today cleared New York City's chief medical examiner of allegations that he covered up police brutality.

The examiner, Elliot R. Gross, said he would file a libel suit against The New York Times, which raised the allegations in a four-part series by Philip Shenon in January.

In a 600-page report, the commission, appointed by Mayor Edward I. Koch, declared Gross "not guilty" of obstructing justice or falsifying medical reports, as alleged by members of his staff and outside pathologists interviewed by The Times.

It found, however, that Gross had made significant "errors" in several autopsies involving victims of alleged police violence and that several cases were "mishandled," according to attorney Arthur L. Liman, the panel chairman. The report also cited mutual mistrust between Gross and his staff and recommended that the office be placed under an independent commission.

In a statement, The Times' metropolitan editor, Peter Millones, said, "The articles in The Times contained many allegations by specifically identified members of the medical examiner's staff and others. The Times felt that these allegations should be brought to public attention. That is the traditional and proper role of a newspaper. Our role stopped there."

Investigations by the state health commissioner and a panel of city officials concluded last month that the medical examiner's office was "understaffed, undertrained, underequipped and underfinanced." The state investigators are expected to make their report on Gross within a few weeks.

Liman's commission of nine lawyers and five pathologists subpoenaed 156 witnesses, took more than 5,800 pages of sworn testimony and reviewed 100,000 documents. Its report said the accusations by Gross' staff members were symptomatic of an office that had become "a den of suspected intrigue and counterintrigue" since Gross took over five years ago.

Gross was appointed by Koch to replace Dr. Michael Baden, who, under civil service rules, then became his deputy. Baden filed suit against him and the city seeking to be reinstated as chief medical examiner. Gross attributed the allegations in The Times to "a malicious campaign of slander" by Baden.

It "was an office devoid of collegiality; a staff frustrated, rebellious and suspicious of its head; and a chief mistrustful of, and lacking confidence in, many of his subordinates," the commission report said in recommending oversight by an independent commission outside civil service requirements.

The panel's pathologists concluded that Gross had mishandled the case of Michael Stewart, a 25-year-old graffiti artist who died in September 1983, allegedly after being beaten by transit police. Three transit officers are under indictment for criminally negligent homicide and perjury and three others for perjury in connection with the case.

The panel said Gross, in amending his preliminary finding of cardiac arrest as the cause of death, should not have relied on a neuropathology consultant's determination that Stewart died of a spinal cord injury. But it called his failure to attribute the death to beatings "an honest mistake," noting that Gross conducted a 6 3/4-hour autopsy in the presence of the Stewart family pathologist and had cooperated fully with the district attorney's office in prosecuting the officers.

Another case involved Mark Safdie, 32, a Brooklyn store owner allegedly beaten and asphyxiated by police as he was being taken into custody after a psychotic episode. Gross attributed the death primarily to "manic-depressive psychosis with acute violent behavior." His former associate medical examiner on the case was quoted in the newspaper series as saying that Gross had pointed out a neck cartilage fracture and called it "a classic case of strangulation." However, the commission said that the associate, Dr. Joan Obe, reexamined the specimen on videotape and said there was no fracture and that she had confused it with another case.

Gross has been on leave since Jan. 29 to defend himself against the allegations, which prompted five city, state and federal investigations. In a statement issued through his lawyer, he said he was "elated" by the commission report.