The Senate Judiciary Committee has warned the Justice Department that it will hold up all pending nominations until the department complies with the law on nomination procedures.

At issue is the department's actions in an appointment to the U.S. Parole Commission, an independent agency within the Justice Department.

There are two problems, which are related, with the nomination: first, the Justice Department nominated the candidate for one position and then attempted to place him in another.

Then, to make this second position available, the department notified a current commission member, a Democrat, that he was being fired even though he has more than two years remaining in his six-year term.

This week Sen. Joseph R. Biden Jr. (D-Del.), a member of the Judiciary Committee, went to Chairman Strom Thurmond (R-S.C.) and asked him to hold up all nominations pending before the committee until the situation can be resolved.

Biden said yesterday that he does not want a precedent set of nominating persons for one job when they might be put into another. "I don't trust them at all. We might find the U.S. attorney for Florida in Duluth, Minn.," he said.

He described the effort to fire the Democratic commissioner as "bush league."

"What . . . difference does it make on the Parole Commission if you're a Democrat or a Republican?" he asked. "It's not a political job."

Thurmond said yesterday, "Sen. Biden has raised what appears to be a valid point concerning the nominating process. I feel certain however that we can resolve the problem with the Department of Justice."

Nominations scheduled for action last week included Alan Nelson for head of the Immigration and Naturalization Service, Robert H. Bork to the Circuit Court of Appeals, two district court judges, four U.S. attorneys and six U.S. marshals. Committee sources say there are many nominations backed up behind those.

The dispute stems from the administration's nomination in November of Benjamin F. Baer to replace Commissioner Joseph A. Nardoza, a Republican whose term expired three years ago. Nardoza's opening is in Philadelphia.

In December, about the time Baer was routinely confirmed by the Senate, Commissioner O.J. Keller, who works in the Washington office, was called by Deputy Associate Attorney General Jeffrey Harris and informed that the attorney general had decided to recommend to President Reagan that Keller be removed from the commission, and that Baer replace him rather than Nardoza in Philadelphia.

A letter from Associate Attorney General Rudolph Giuliani later in the month confirmed that Baer would take Keller's position effective March 15. In addition, Justice Department sources confirmed that there were plans to replace all six Democrats on the nine-member commission, even though they have fixed terms.

But Keller, who has 2 1/2 years remaining in his term, refused to resign, and filed a lawsuit against the administration. He called the situation "rotten politics. It's the spoils system at its worst."

When Keller asked in federal court here for a temporary restraining order a spokesman for the Justice Department said that the final decision had not been made to fire him.

Meanwhile, a preliminary legal opinion requested by the Senate Judiciary Committee says Justice does not have authority to fire Keller.

The opinion, prepared by the Congressional Research Service of the Library of Congress, concluded that a parole commissioner "performs quasi-judicial and quasi-legislative functions and that Congress intended that the commission be insulated from executive control in the performance of those functions."

An aide to Thurmond called Justice to find out what was going on, and on Thursday the department sent a letter to Thurmond saying that in fact Baer was replacing neither Nardoza nor Keller. Instead, it said that he will take the place of Richard Mulcrone, who recently resigned as regional commissioner in Kansas City.

Biden said Justice will be able to clear up the situation either by putting Baer in Nardoza's position in Philadelphia or resubmitting his name for confirmation for the Kansas City opening.

The Parole Commission operates independently within Justice, and has the power to deny or approve parole applications, issue regulations and create regional offices.