An FBI informer who was one of Secretary of Labor Raymond J. Donovan's unidentified accusers has been indicted on charges of obstruction of justice and lying to FBI agents about alleged ties between Donovan and organized crime.

A federal grand jury in Syracuse, N.Y., accused Michael Klepfer, 42, a trucking company executive, of repeatedly making false statements to FBI investigators during the course of Donovan's Senate confirmation hearings in 1981 and again last year during special prosecutor Leon Silverman's investigation.

The four-count indictment was unsealed in U.S. District Court in Syracuse Thursday afternoon after Klepfer surrendered to federal authorities. He pleaded not guilty and was released on $40,000 bond.

Klepfer's name had been kept a closely held secret throughout the investigations. Silverman was not told who Klepfer was during the first phase of his investigation because the FBI counted him among a number of informers "whose lives . . . would be jeopardized if their identities became known."

"Accordingly," Silverman said in his first report last June, in a section dealing with a number of Klepfer's allegations, "the special prosecutor received only the information, not the identity of the anonymous informant."

The indictment accuses Klepfer of falsely claiming personal knowledge of ties between Donovan and a now-deceased New Jersey mobster, Salvatore Briguglio, and of lying about purported conversations with another New Jersey hoodlum, Fred Furino, concerning Donovan.

Furino, who once worked at the Canny Trucking Co.'s Elizabeth, N.J., terminal and was allegedly a sometime "bagman" for Briguglio, was found dead in the trunk of his car in New York City last June 11.

According to the indictment, Klepfer subsequently told FBI agents that Furino was killed to keep him from telling federal authorities that Donovan had funneled $20 million from the Teamsters union into the 1980 Ronald Reagan presidential campaign and that, in turn, Donovan was to recommend presidential pardons for two imprisoned felons, organized crime boss Russell Bufalino and former Teamsters union official Anthony (Tony Pro) Provenzano.

All that, the grand jury charged, was false.

Justice Department officials said they believed the indictment was unprecedented. They could not recall any FBI informer ever being prosecuted for what he said as an informer. Sources said that Klepfer was offered government protection after being arraigned Thursday, but he declined it.

The indictment also accused Klepfer of lying in January, 1981, while Donovan was undergoing stormy confirmation hearings, by telling FBI agents that Donovan had engaged in a bid-rigging operation on behalf of his New Jersey construction company with the help of inside information supplied by Briguglio.

An FBI memo containing that allegation, which came to light last year, described Klepfer anonymously as a source who "has furnished reliable information to the FBI over a period of six years, all of which has always been found to be highly credible."

By the time Silverman finally concluded his investigation last September, however, Klepfer, though still anonymous, had retracted every one of the charges he made. Silverman alluded to him as an informant who had recanted in an FBI interview last Sept. 8 "in the face of an impending polygraph examination."

The special prosecutor said a polygraph test was administered anyway, "to determine whether the recantation was truthful." As Silverman put it at the time, the test showed that "the informant was truthful when he said he had deliberately lied . . . ."

Silverman closed his investigation last Sept. 13, saying that he had investigated a batch of new allegations against Donovan and once again concluded that there was "insufficent credible evidence" to support any criminal charges.

The special prosecutor refused at the time, however, to spell out which of the allegations represented the-then anonymous informer's "deliberate lies."

It was the second indictment this week to grow out of the Donovan investigation. On Tuesday, a federal grand jury in Brooklyn indicted two former labor union officials, Louis Sanzo and Amadio Petito, for lying under oath about "no show" jobs on a New York subway construction project that Donovan's company had undertaken. They were accused of perjury, obstruction of justice and conspiracy to impede Silverman's investigation.

Klepfer faces a maximum of five years in prison and fines varying from $5,000 to $10,000 for conviction of each count against him.

Other false accusations he made, according to the indictment, included claims that:

* Furino told him of two "bagmen" for Briguglio who made pickups of money from Donovan and that Furino said that he, Furino, had also done so.

* Furino told him that Donovan's company, Schiavone Construction, had provided building material for Briguglio's home.

* Klepfer himself saw Briguglio and an individual who Briguglio later identified to Klepfer as Donovan at a Fort Lee, N.J., restaurant on April 18, 1969.

* Donovan socialized on a regular basis with Briguglio, Furino and another Teamsters official in Union City, N.J., nightclubs, that Briguglio and Donovan had grown up together, and that Briguglio accompanied Donovan on pleasure trips to various locations.

* Donovan's company provided building material for Provenzano's home in the mid-1960s as a result of Donovan's association with Briguglio, a onetime business agent in Provenzano's Teamsters Local 560.

* It was Furino who told Klepfer of the bid-rigging scheme purportedly involving Donovan and Briguglio.

All these allegations, the grand jury said, were "false, fictitious and fraudulent."