U.S. District Court Judge Thomas A. Flannery refused yesterday to halt the trial of former White House aide Lyn Nofziger despite a federal appeals court decision that the independent counsel law is unconstitutional.

"We're going to try this case to a conclusion," Flannery told lawyers for Nofziger when they sought a dismissal. "I haven't read the opinion. I'm not going to consider it at this time."

Nofziger and Mark A. Bragg, Nofziger's partner in a Washington consulting firm, went on trial Tuesday on federal conflict-of-interest charges brought by independent counsel James C. McKay.

McKay was appointed last Feb. 2 by a special three-judge court acting under provisions of the Ethics in Government Act that were held unconstitutional yesterday.

On March 6, McKay accepted a backup appointment as a Justice Department prosecutor in light of the mushrooming litigation over the independent counsel act.

Renewing their unsuccessful argument of last fall, attorneys for Nofziger and Bragg said yesterday that their clients may have been prejudiced by McKay's work during his 32 days as solely a court-appointed prosecutor.

Some documents were subpoenaed then, and McKay appeared once before the grand jury that indicted Nofziger and Bragg last July.

Flannery, who held the independent counsel law constitutional in pretrial hearings last month, said he does not intend to reenter that discussion. If Nofziger and Bragg are acquitted, he said, that would settle the matter.

The trial itself slowed yesterday in drawn-out bench conferences and a dispute about the extent of testimony to be permitted before the jury by a key prosecution witness, Mario E. Moreno, former executive vice president of the Wedtech Corp.

Nofziger, former director of political affairs at the Reagan White House, has been accused of illegally lobbying former friends there in 1982 for Wedtech and two other clients.

Nofziger and Bragg, indicted on one count of aiding and abetting, received $234,595 in cash and $651,750 in stock-sale proceeds before the Bronx-based defense company went bankrupt last year.

Defense lawyers contended that the two received only $52,000 for their Wedtech lobbying in 1982, when the company won a lucrative Army engine contract and that this was all that jurors should hear.

In a dress rehearsal without the jury, Moreno testified that he and Wedtech founder John Mariotta agreed in January 1983 to give Nofziger and Bragg one percent of stock that Wedtech was planning to issue when it went public later that year.

A Colombian-born businessman who has pleaded guilty to paying bribes and looting Wedtech of hundreds of thousands of dollars, Moreno said he and Mariotta promised the stock to Bragg at a meeting at which Bragg chided them for falling behind on agreed-upon fees for 1982.

"Mr. Bragg indicated he was very disappointed with the company . . . that we were more or less like a welfare case . . . that other companies were paying fees of $300,000 {to Nofziger and Bragg}, but they were doing much more work for us," he said.

Moreno said that Wedtech had planned to go public if it won the Army contract and that the idea had been mentioned to several people, "probably including" Nofziger and Bragg. He said he and Mariotta decided to give them the stock "for past services, primarily on the engine contract" and to keep them working for Wedtech.

Flannery ruled that Moreno could testify before the jury Monday about the stock grant without mentioning the exact percentage or how much Nofziger and Bragg eventually made on its sale. Flannery also said the jury should not hear about $300,000 fees paid by other clients.