The son of a reputed mobster involved in the investigation of Secretary of Labor Raymond J. Donovan was shot to death Wednesday night in the Bronx in what appeared to be a gangland-style execution.

The victim, Nat Masselli, 31, was killed, according to authorities, when a passenger in the car Masselli was driving fired a bullet into the back of his head, just behind his right ear.

The FBI immediately stepped into the case at the request of Leon Silverman, the special prosecutor in charge of the Donovan inquiry.

"I am disturbed that anybody who is involved in my investigation should be murdered, and I have asked the FBI to conduct an intensive investigation to see whether that murder is linked to this investigation," Silverman said.

Nat Masselli and his father, William P. Masselli, reputed by the FBI to be a member of the Genovese family of the Mafia, were questioned extensively by Silverman and his investigators earlier this year about their associations with Donovan as a New Jersey construction company executive.

Both Massellis had been active in an excavation company, Jopel Construction and Trucking, that served as a subcontractor for Donovan's firm on a number of New York City subway projects.

Jopel has come under renewed investigation by New York City officials for charging the city some $468,000 for dirt that it had removed from a subway project in Queens. Donovan's company, Schiavone Construction, was the prime contractor and under its contract with the New York Transit Authority, the city was entitled to the dirt "without cost."

Authorities in New York said Nat Masselli was killed around 8:20 p.m. Wednesday while driving his 1977 Lincoln Continental through a residential neighborhood alongside Van Cortlandt Park in the Bronx. A witness said that one or two other men were in the car with him.

A spokesman for Bronx District Attorney Mario Merola said Masselli died of a bullet wound in the right side of his head, behind the ear. Police said his car veered out of control and ran into a parked car in the 3400 block of Van Cortlandt Park East.

One or two men reportedly jumped out of the Lincoln and got into a red car, driven by another man, which had been trailing behind. A motorist who had been in the parked car rammed by the Lincoln telephoned police. Masselli, who lived in Scarsdale, was dead by the time an ambulance arrived.

It was the second mob-style slaying of a witness in the Donovan case this year. In June, Fred Furino, an alleged Mafia "bagman" who testified before a grand jury twice about alleged connections with Donovan, was found dead in the trunk of his own car in lower Manhattan, with a bullet hole in his forehead.

Silverman refused yesterday to say whether he had recently interviewed or sought to interview either Nat or William Masselli. The special prosecutor had virtually wrapped up his investigation in late June by announcing that he had not found enough "credible evidence" to warrant a prosecution of Donovan. Within a few weeks, however, Silverman reopened the inquiry in light of additional allegations that he said had come to his attention.

At least one of those allegations, sources say, concerns the longstanding but never-substantiated claim that Donovan had met with Masselli and perhaps other organized crime figures during the 1979 Super Bowl weekend in Miami.

Donovan has steadily denied any such links. Testifying at his Senate confirmation hearings in 1981, he said he was unaware of Masselli's organized crime ties and declared that they had spoken to each other no more than three times over the years, always about business matters.

Months later, the FBI disclosed that it had overheard mention of Donovan, in a social context, in the course of a wiretapped conversation that took place in 1979 between William and Nat Masselli. By then the target of an intensive organized crime investigation, the elder Masselli was telling his son about how he had gotten an invitation from another Schiavone executive, Al Magrini, to fly to some event with "Ronnie Ronald Schia-vone, president of Schiavone Construction and Ray Donovan."

William Masselli, now 55, started serving a seven-year federal prison term in February following his conviction on other charges, unrelated to Donovan, that stemmed from the wiretap. A few weeks before he went to prison, however, he approached Schiavone officials with contentions that Schiavone Construction still "owed him a lot of money" and that he needed some $40,000 to pay off court-imposed fines.

According to Silverman's report in June, Schiavone lawyer Morris Levin quoted Masselli as having told him last Jan. 4 that "I'm suppose sic to go away Monday, but I don't have to if I help the government . . . . They will help me if I give them anyone in Schiavone Construction."

After William Masselli went to prison, Nat Masselli appears to have carried on Jopel's business under a new name, the Red Apple Equipment Co., which was incorporated last Feb. 24. New York Transit Authority officials said Red Apple, which used the same phone number at Masselli's Bronx warehouse, had picked up Jopel's subway contracts.