Lawyers for Labor Secretary Raymond J. Donovan and his company have protested that they are being prosecuted for what has become a common practice in dealing with minority business subcontractors nationwide.

The claim was made in papers filed Thursday in Bronx Supreme Court, where Donovan and codefendants including seven executives from his New Jersey construction company are engaged in pretrial efforts for dismissal of an indictment charging them with fraud and grand larceny on a subway project.

In one document, Dewey Thomas Jr., executive director of the National Association of Minority Contractors here, said more than eight out of 10 disadvantaged or minority business enterprises (MBEs) in a recent "sample survey" said they lease equipment from prime contractors for whom they work.

Sixty-two percent of them involved in heavy construction, he said, lack sufficient capital to purchase necessary equipment.

Bronx authorities have accused the defendants of conspiring to defraud the New York City Transit Authority of about $7.4 million on the subway project by pretending to rent specialized equipment to a mob-controlled subcontractor posing as a legitimate MBE.

Thomas said his association strongly opposes "front" MBE companies but is concerned about the Donovan case, saying it has created uncertainty about leasing arrangements between minority and nonminority contractors.

In a Dec. 31, 1984, letter to Thomas, which Donovan's lawyers also filed, Transportation Department general counsel Jim J. Marquez indicated that it would be proper for a prime contractor to provide certain specialized equipment to a legitimate minority subcontractor if the minority company performed the work.

Bronx prosecutors had no comment on the defense motion. They have charged that Jopel Contracting, the subcontractor involved in the indictment, was a phony MBE and never controlled equipment it supposedly was leasing from Donovan's firm.