Secretary of Labor Raymond J. Donovan's lawyers protested in U.S. District Court in New York yesterday that the Bronx grand jury that indicted him had been inadequately schooled in conspiracy law.

Donovan's attorneys said instructions given to the grand jury by Bronx prosecutors, "among other deficiencies," failed to include an explanation of what circumstances would make Donovan a member of the alleged conspiracy. Donovan was indicted on conspiracy charges Sept. 24.

Citing state grand jury records turned over to them last week, the Donovan lawyers made the argument in a final brief and related pleadings seeking to have the case against him separated from that of the other defendants and moved from Bronx Supreme Court into federal court.

U.S. District Court Judge Lloyd F. MacMahon has held four days of hearings on those issues. He indicated that he would rule early next month. Prosecutors for Bronx District Attorney Mario Merola are to file their final response Jan. 2.

Donovan and nine other men, including seven executives from his New Jersey construction company, have been accused of scheming to steal $7.44 million from the New York City Transit Authority on a $186 million subway project.

Companies allegedly involved in the scheme, Schiavone Construction Co., where Donovan was executive vice president before joining the Reagan Cabinet, and Jopel Contracting & Trucking, a Bronx-based subcontractor that represented itself as a minority business enterprise, also were indicted.

Donovan attorneys William O. Bittman and Paul J. Curran argued in the papers filed yesterday that there was an "almost total lack of evidence to connect . . . Donovan to the alleged conspiracy," consisting primarily of a $200,000 check that Donovan cosigned in March 1979 to get Jopel started on the job.

They also complained that "the legal instructions given to the grand jury did not mention any amount of money involved in the alleged larceny, nor any explanation of 'conspiracy theory.' "

In addition, the Donovan lawyers said the instructions "did not explain that before the grand jury can consider the acts and statements of Secretary Donovan's alleged co-conspirators or co-participants in indicting Secretary Donovan, it must first find that it is able to connect . . . Donovan to the alleged conspiracy by competent evidence of his own acts and statements."

Bronx prosecutors have maintained that evidence against Donovan, ranging from the $200,000 check to various "inconsistent and false statements" he made in the course of several investigations and other circumstantial evidence, is sufficient to link him to the alleged conspiracy.

According to the prosecution, it centered on a scheme in which Schiavone Construction purchased special equipment for the subway project, pretended to rent it to Jopel, and then had Jopel generate phony bills that the Transit Authority paid as if the money was being dispensed in satisfaction of minority-business requirements.

Bittman and Curran, however, asserted that "no evidence before the grand jury showed that Secretary Donovan had any knowledge of, or participated in, any such alleged scheme."

Donovan's lawyers argued that he was entitled to have his case removed to federal court under a long-standing federal statute originally enacted to protect federal customs agents in the performance of their duties.

The attorneys said it was clear that the Bronx proceedings have interfered with the operations of the federal government in that "Secretary Donovan was forced to take a leave of absence without pay" as a result of the indictment.