The FBI "misled" the Senate Labor and Human Resources Committee in its consideration of the nomination of Labor Secretary Raymond J. Donovan and withheld pertinent allegations in the case for almost two years, according to a special staff report to be issued by the committee.

The charges are leveled in an extensively footnoted report, supplemented by an 885-page appendix, that focuses on the performance of the FBI executive assistant director, Francis M. (Bud) Mullen Jr., now acting chief of the Drug Enforcement Administration.

The study accused Mullen and other FBI officials, including Director William H. Webster, of a lack of care and candor in pursuing alleged ties between Donovan and organized crime and informing the committee about them in a timely fashion. Some charges were glossed over and others were ignored completely, the report said.

"In short," the report concluded, "the FBI supplied information that was inaccurate, unclear and too late. Worse, while the FBI told the committee that there was nothing else to know, it withheld 'pertinent,' 'significant,' and 'important' information."

As a result, the committee investigation said, "the FBI usurped the Senate's constitutional responsibility; it guaranteed that no senator's consent would be adequately informed."

The findings were set out in a report by special committee counsel John P. Flannery II that the committee had authorized for release this afternoon. Any immediate impact is likely to be felt in the Senate Judiciary Committee, where Mullen's nomination as DEA administrator has been in limbo, awaiting the conclusion of the Labor Committee's inquiry.

The 46-page report, which implied that the staff investigation might not be over, emphasized that it was not directed at the truth or falsity of the allegations against Donovan--allegations that a special prosecutor dropped last fall because of "insufficient credible evidence." The committee, however, said it wanted to know "why the FBI told it about some allegations but not at all about others."

The most glaring omission, the study said, concerned a Jan. 11, 1981, teletype from the FBI's New York office to FBI headquarters here, addressed to the "immediate" attention of Webster. Donovan was due to testify before the Labor Committee the next morning for the first time.

The telex stated that on Jan. 10, an FBI source who had "provided reliable information in the past," had made four allegations involving Donovan and his firm. One was that Donovan, then executive vice president of a New Jersey construction company, had "definite ties to LCN (La Cosa Nostra) figures in a liaison capacity" in dealings with various trade unions.

The informant maintained that "the relationship between Schiavone Construction Donovan's company and Big J Demolition should be explored in that in order to do business with Big J Demolition . . . one had to have LCN connections."

The Senate study noted that the owner of Big J "has an arrest record and FBI number as do other Big J personnel" and, in addition, Schiavone Construction rented equipment from Big J in the course of its work on the 63rd Street subway project in New York.

The staff study said the Labor Committee was not informed of the "Big J" allegations until December, 1982, months after the special prosecutor had gone out of business and almost two years after the memo had been sent to FBI headquarters. "There is no evidence," the report stated, "of any FBI investigation of the Big J allegations."