Barnet D. Skolnik, the assistant U.S. attorney who successfully prosecuted former Vice President Spiro T. Agnew and Maryland Gov. Marvin Mandel, has agreed to head the prosecution team in the stalled investigation of FBI "black-bag" jobs.

Justice Department officials refused to comment officially on the matter yesterday. They said only that an announcement is expected today, naming members of an expanded task force to replace the five attorneys who suddenly resigned from the controversial FBI investigation last week after a sharp dispute with Attorney General Griffin B. Bell.

Other Justice Department sources in Washington said, however, that Skolnik - who gained a reputation as a hard-nosed prosecutor in the highly publicized Maryland political corruption cases - was asked last weekend to take on the new task.

According to the sources, Skolnik will head the prosecution team and Paul R. Boucher, deputy chief of the Criminal Division's general crimes section, will direct the new investigating task force.

Skolnik declined comment yesterday. "I just can't talk about this," he said. Boucher could not be reached for comment.

The move to bring Skolnik into the case was viewed by some department officials as a sign that Bell is finally serious about tackling the sensitive investigation.

"The judge (Bell) means business," said one official knowledgeable about Skolnik's selection.

So far, only former FBI supervisor John J. Kearney has been indicted in the 18-month investigation of alleged FBI break-ins, wiretaps and mail-openings against radical fugitives in New York in the early 1970s.

The previous task force, headed by William Gardner of the Civil Rights Division, asked to be relieved of responsibility in the case when Bell refused to follow its recommendations and approve the indictment of other FBI officials.

Bell explained that he had wanted to see what issues would be raised at the Kearney trial before proceeding with more prosecutions, but he admitted last week that delays in the trial have closed that option.

Instead, Bell and his top adviser on criminal matters, Benjamin R. Civiletti, have decided to accelerate the pace of the investigation, which has been stymied because of the simmering disagreement between Bell and the old task force.

Sources familiar with the case said the federal grand jury in Washington charged with hearing evidence in the case has done nothing on the FBI cases in the last two months.

The attorneys who resigned from the investigation are known to feel that it is unfair to try Kearney alone when other FBI officials, including some superiors at Washington headquarters, passed on the directives for the allegedly illegal activities.

The Kearney case has been bogged down for months because fo complicated pre-trial motions by his attorney, Edward Bennett Williams.

The judge has granted Williams' request for a wide range of documents, Williams apparently hopes to find evidence to show that the wiretaps and mail openings Kearney is charged with were necessary because the targeted Weather Underground members were somehow backed by a foreign power.

Bell's public statements of concern about this turn in the Kearney trial have led to speculation he might drop the case. But it is considered unlikely that Skolnik would be called on just to handle a plea-bargain arrangement or dismissal after discovery.

It was not clear yesterday whether Skolnik would leave his post as an assistant U.S. attorney in Baltimore or simply be detached for the work on the FBI investigation.

Skolnik has said since the Mandel verdict in September that he was interested in leaving the Justice Department to enter private practice.

But it is known that Civiletti, who also is a former assistant U.S. attorney in Baltimore, has tried before to persuade him to stay on as a federal prosecutor. One offer Skolnik reportedly rejected was to become chief of one of the department's organized crime strike forces.