A 66-year-old man who authorities said was a member of a New York Mafia family was arrested yesterday in the mob-style slaying of a witness in the investigation of Labor Secretary Raymond J. Donovan.

Salvatore Odierno of Valley Stream, N.Y., was charged with second-degree murder. He pleaded not guilty at his arraignment in Bronx Criminal Court yesterday afternoon.

Investigators for Bronx District Attorney Mario Merola said Odierno surrendered around 10 a.m. yesterday after he had been linked to the homicide by a license plate number that a witness had recorded.

The victim, Nat Masselli, 31, was shot to death Wednesday night when a passenger in the car Masselli was driving in the Bronx shot Masselli in the back of the head. Witnesses said one or two men jumped out of Masselli's Lincoln Continental and drove off in a red car that had been trailing behind.

Odierno was ordered held without bail and was put in a cell by himself.

Assistant District Attorney James Shalleck described Odierno as a member of an organized crime family "with no legal source of income" and asked that he be put in protective custody "for the defendant's safety."

Shalleck said Odierno had been arrested nine times, dating back to 1938, but Odierno's attorney, Louis Aidala, said his client had been convicted only twice, once in 1940 and again in 1980 for contempt of court.

At the time of the Masselli killing, Nat Masselli's father, William P. Masselli, 55, was waiting to be called before a federal grand jury assigned to the Donovan investigation. William Masselli, a reputed member of the Genovese family of the Mafia, was transferred to New York Tuesday from an upstate federal prison.

Sources said Odierno was a sidekick of Philip Buono, who was once listed on the payroll of Masselli's wholesale meat company in the South Bronx.

Merola said Odierno is "well-known as an individual who has survived life in a very hazardous profession," while Aidala described his client as "a retired gentleman. He did not run and he did not hide. He has nothing to worry about."

The special prosecutor in charge of the Donovan investigation, Leon Silverman, has been investigating charges that Donovan, before joining President Reagan's Cabinet, had social relationships with William Masselli and other reputed members of organized crime.

Buono was one of those questioned about alleged social relationships involving Donovan at the 1979 Super Bowl in Miami. Silverman was investigating allegations that Donovan had met with Masselli and other reputed gangland figures that week.

Buono was granted immunity for an appearance before the grand jury earlier this year, but apparently imparted no significant information.

Donovan has steadily denied any such associations. Silverman, however, has continued to investigate the reports.

In addition to his wholesale meat business, William Masselli was president and chief operating officer of Jo-Pel Construction and Trucking Co., an excavation firm that grew into a multimillion-dollar-a-year business as a subcontractor for Donovan's company, Schiavone Construction, on a series of New York City subway projects.

Nat Masselli had also been questioned in the Donovan inquiry, and at one point last spring he assisted Silverman's investigators in a wiretapping assignment.

The younger Masselli served as office manager and bookkeeper for Jo-Pel before his father went to prison last February. Since then, he had been helping to carry on the business under a new name, the Red Apple Equipment Co.

Nat Masselli was killed the night after his father was transferred from an upstate federal prison to Manhattan's Metropolitan Correctional Center on a writ obtained by Silverman's office.

The FBI stepped into the homicide case at Silverman's request to try to determine whether the Nat Masselli killing was intended, as one source put it, as "a signal to the old man" to keep him from talking.

Another source close to the investigation suggested that the homicide may have followed an argument over what had happened to Jo-Pel's assets when William Masselli went to prison. In any case, authorities were reportedly continuing to search for two other suspects.

Silverman refused yesterday to say whether Odierno had any connections with individuals involved in his investigation. He said he was "gratified that the investigation of the FBI and the police has produced such quick results," but he declined further comment.