A special federal court indicated yesterday that it will name an independent counsel to investigate the lobbying activities of Michael K. Deaver, the former White House deputy chief of staff.

The Justice Department formally requested the appointment last Thursday, and the request was disclosed yesterday by a three-judge panel of the U.S. Court of Appeals here. The judges did not say when they would name the independent counsel, but the appointment is expected soon.

Deaver and five Democratic senators had asked the Justice Department to seek such an outside probe of allegations that Deaver may have violated conflict-of-interest laws in leaving the White House last May and building up his multimillion-dollar Washington consulting firm. Two other agencies -- the General Accounting Office and the Office of Government Ethics -- have referred allegations involving Deaver to the Justice Department.

A similar referral to Justice, this one relating to a member of Deaver's firm, was made last week by the U.S. Trade Representative's office.

"Mr. Deaver is pleased that the process toward a fair hearing is on course," his spokeswoman, Pamela G. Bailey, said yesterday. She said Deaver believes "that such a counsel is the only appropriate way to have the various allegations fully and impartially reviewed."

The scope of the Deaver inquiry will not be known until the independent counsel is appointed. A one-page order, issued by Judges George E. MacKinnon, Lewis R. Morgan and Walter R. Mansfield, said the Justice Department can release its report to the court, which outlines the department's reasons for requesting the independent probe, at the "time of appointment of independent counsel."

The independent counsel, who would be the sixth named under the 1978 Ethics in Government Act, is certain to look into Deaver's $105,000-a-year contract with the government of Canada. The GAO told a House subcommittee this month that Deaver may have violated the law by representing Canada on the issue of acid rain, which he had discussed in numerous White House meetings while preparing for a 1985 U.S.-Canadian summit.

GAO officials questioned whether Deaver violated the lifetime legal ban on a senior federal official lobbying the government on an issue in which he had personally and substantially participated. They also questioned whether Deaver violated the prohibition on a former official lobbying his former agency on any matter for one year after leaving government.

The decision to seek an independent counsel was made by Deputy Attorney General D. Lowell Jensen after Attorney General Edwin Meese III disqualified himself from the matter, citing his longtime association with Deaver.

The Senate Democrats' letter asked that the outside probe include three other areas. One was Deaver's efforts on behalf of Rockwell International to persuade the Reagan administration to build more B1 bombers. Deaver discussed the subject with James C. Miller III, director of the Office of Management and Budget.

The second issue was Deaver's work for Daewoo Corp., a South Korean conglomerate, which included 28 contacts in four months with senior Treasury Department officials in an effort to settle a $25 million Customs fraud case. The senators also cited Deaver's lobbying for retention of tax breaks for U.S. companies that do business in Puerto Rico.

It is not known whether the Justice Department urged investigation of these and other issues in its report to the court. The preliminary FBI probe aimed at determining whether to seek an independent counsel, for example, also examined Deaver's involvement in obtaining a letter from President Reagan in support of the D.C. Baseball Commission's effort to bring a major league team to Washington.

The Justice Department also received evidence last week from the U.S. Trade Representative's office, which has completed an internal inquiry into a former senior trade official who works for Michael K. Deaver & Associates. Trade office spokesman Gary Holmes said the agency's general counsel asked all office employes whether they had contacts with the former senior official, Doral S. Cooper, and has forwarded the results to Justice.