Government prosecutors said yesterday that the death Tuesday of a potential witness against former CIA agent Edwin P. Wilson will have no effect on their ability to prosecute Wilson next month.

Wilson, who is being held at an undisclosed location on $60 million bond, is scheduled to go to trial in federal courts in Alexandria, Washington and Houston on charges that he shipped weapons and explosives to Libyan ruler Col. Muammar Qaddafi. The first trial, in Alexandria, is slated to begin Nov. 15.

The witness, Kevin P. Mulcahy, a former CIA technician who later worked for Wilson, died Tuesday of unknown causes outside his motel room near Edinburg, Va., about 90 miles west of Washington.

"Kevin's death, as sad and as tragic as it is, is not going to affect our prosecution in any way," said Assistant U.S. Attorney E. Lawrence Barcella Jr., who has supervised the government's investigation into Wilson's activities since 1976.

Since that investigation began, the government has amassed extensive documentary evidence concerning Wilson's alleged business dealings with Libya and has obtained the cooperation of several of Wilson's key associates.

With the development of that evidence, Mulcahy's role as a witness in the case has diminished considerably, law enforcement sources said. It had been expected that Mulcahy's principal role would be as a witness only at the trial in Washington, and not in court proceedings in the other cities.

Others familiar with the case against Wilson said they believed that Mulcahy's death might cause the prosecutors problems with using as evidence documents that Mulcahy took from Wilson's office here and turned over to the CIA in September 1976.

One problem might arise, the sources said, in proving that the documents did in fact come from Wilson's office. If that cannot be established, and the documents are not verifiable without Mulcahy's testimony, then it is possible the court could prohibit the government from using them as evidence against Wilson.

It was not clear yesterday which, if any, of those documents prosecutors intended to try to use in the trial. Barcella declined to comment on whether any evidence would be affected by Mulcahy's death.

Mulcahy first tipped the CIA in September 1976 to alleged arms dealing and terrorist training in Libya by Wilson and other former CIA employes. Wilson was indicted in federal court in Washington in April 1980 on charges of shipping explosives and timing devices to Libya and conspiring to assassinate a Libyan dissident on behalf of Qaddafi. U.S. District Court Judge John H. Pratt ordered a trial on the explosives charges to begin here Nov. 22, but has not set a trial date on the conspiracy charges. Mulcahy, according to informed sources, was not going to be a witness in the conspiracy case, but did have firsthand information about the explosives shipments in 1976 and may have been called to testify in that part of the case.

The charges against Wilson in Alexandria involve four handguns Wilson allegedly ordered associates to purchase here and turn over to a Libyan official in Bonn in the spring of 1979, almost three years after Mulcahy left Wilson's employment. One of those handguns was used a year later in the assassination of a Libyan dissident in Bonn, according to investigators.

The Houston indictment charged Wilson with shipping 20 tons of C-4 plastic explosives to Libya in October 1977, more than a year after Mulcahy left Wilson's operations.