A key witness in the government's probe of Drexel Burnham Lambert Inc. financier Michael Milken yesterday settled Securities and Exchange Commission charges that he falsified accounting records.

Setrag Mooradian, who was the chief in-house accountant for former stock speculator Ivan F. Boesky, was suspended from the securities industry for one year by the SEC. Mooradian, without admitting or denying the SEC's charges, pledged to continue his cooperation with government investigations as part of his settlement.

Mooradian has testified for the SEC and before a federal grand jury in Manhattan in probes of an alleged illegal stock trading arrangement between Boesky and Milken, according to sources familiar with the investigations. Milken heads Drexel's influential junk bond department in Beverly Hills, Calif.

As previously reported, the government is examining evidence that Boesky illegally "parked" stock for Milken during a 1984 takeover of Fischbach Corp. by Drexel client Victor Posner. A stock is "parked" when one party holds shares for another without assuming the market risks of ownership.

Drexel has said repeatedly that it has found no evidence of wrongdoing by any of its employes and a spokesman reiterated that statement yesterday.

Last April, Boesky pleaded guilty to filing a false statement with the SEC in connection with the Fischbach takeover. Boesky has been cooperating with government investigators since last September, when he finalized his plea bargain and agreed to pay the SEC a record $100 million to settle insider trading charges.

At the center of the government's Milken investigation, which has relied on Boesky's cooperation, is a $5.3 million payment made by Boesky to Drexel in March 1986.

Boesky has told government investigators that the payment was made to reconcile accounts in his illegal stock trading arrangement with Milken, which included trading in Fischbach and at least half a dozen other stocks, according to sources familiar with the probe. Drexel has said the payment was for legitimate investment banking services.

The SEC charged yesterday that Seemala Corp., a broker dealer controlled by Boesky, "acquired and held certain securities of Fischbach Corp. and other issuers in which one or more unaffiliated persons had beneficial interests. Mooradian knew or had reason to know of the beneficial interests of such persons, but caused the books and records of Seemala to be maintained in such a manner as not to reflect these beneficial interests."

Mooradian and his lawyer declined to comment yesterday.

Although the SEC papers did not mention Milken, sources familiar with the government's investigation confirmed again yesterday that Milken is one of the people who allegedly participated in the conspiracy to park Fischbach stock with Seemala.

Sources said yesterday's settlement with Mooradian is a significant step in the government's investigation of Milken and Drexel because it clears the way for possible testimony by Mooradian at a trial.

SEC investigators appear to be attempting to construct a case against Milken that will rely on testimony not only by Boesky, but on documents and evidence provided by accountants at Drexel and Seemala.

Lawyers familiar with the case said yesterday that they have been informed that as part of the effort Charles Thurnher, a record keeper in Drexel's Beverly Hills office, has been granted immunity from criminal charges by federal prosecutors.