Two Brooklyn firms hired as minority business subcontractors on millions of dollars worth of New York public works projects have been ordered disqualifed from minority work on new state Department of Transportation projects, officials said yesterday.

The two Brooklyn companies, however, remain on the approved list of the New York City Transit Authority and have been given more than $5 million worth of work as minority business enterprises (MBEs) by former U.S. labor secretary Raymond J. Donovan's construction company.

One of the firms, Santop Construction, is listed as headed by Sandra Toporoff, wife of a former Transit Authority engineer, Irwin Toporoff. The other, Leskay Construction, is headed by an ex-Transit Authority engineer, Lester Hamilton, who is black.

New York state's assistant commissioner of transportation for legal affairs, Darrell Harp, said reviews of four state-funded projects not connected with the Transit Authority led to the actions against Santop and Leskay.

He said the inquiry showed that Sandra Toporoff "does not appear to run the company in a fashion we consider appropriate for WBE women's business enterprise status." Beyond that, he said, materials in one Santop project "ostensibly . . . were passed through the WBE but it didn't really provide any commercially useful value. All they did was process an account."

On one project assigned to Leskay, Harp said, "There was no record to show that Lester Hamilton ever appeared on the project or that the workmen even knew who he was. They were just payrolled through him."

A state DOT review panel last month reconfirmed a decision to remove Santop from its list of approved contractors, Harp said. He said an earlier panel found Leskay technically capable of performing as an MBE and thus simply ordered it suspended for two years.

Both decisions are subject to appeal. Neither the Toporoffs nor Hamilton could be reached yesterday.

Donovan and his company, Schiavone Construction, are facing criminal trial in the Bronx together with other defendants on charges of using a phony minority business firm, Jopel Contracting, to defraud the Transit Authority of $7.4 million on a midtown subway project.

Leskay was assigned a $2.1 million contract in April 1979 on the same project, records indicate. Santop got $3.6 million worth of MBE work on two other subway projects where Schiavone was general contractor.

A Transit Authority spokesman, Bob Slovak, said yesterday his agency is "in the process of reviewing our minority certification procedures to see if there are any gaping holes any place." He said the review was started "about a month ago."