A large part of the evidence in the case of 12 men who have been charged with drug smuggling here has apparently gone up in smoke, as U.S. agents have already burned most of the six tons of marijuana seized in companion raids on the Eastern Shore last June.

Agents of the Federal Drug Enforcement Administration did save 132 pounds of the marijuana, which was seized in raids in Easton, Md., and Chincoteague, Va. But, in accordance with routine procedure, the remainder of the haul was burned shortly after at an undisclosed location.

Because the burning of the drugs was so routine, U.S. prosecutors were considerably taken aback recently when a federal magistrate ruled that, when they present their case in court, they may not refer to any marijuana other than the 132 pounds they actually have in custody.

Magistrate Frederic N. Smalkin said that he made the ruling because the defense attorneys cannot examine the tons of the drug that were burned. "To allow the government to put on testimonial evidence as to the gross amounts of marijuana seized . . . would deny the defendants their rights effectively to confront the witnesses and evidence against them."

The U.S. prosecutor who will try the case, Catherine Blake, has appealed the magistrate's order to the chief judge of the federal court.

A spokesman for the DEA office in Washington said yesterday that he had never heard of a drug case being contested solely because the bulk of the drugs had been destroyed.

"The agents manual, or the nares' bible, encourages the earliest possible burning as long as it is done in conjunction with the judicial system," spokesman Bill Deac said.

"Think of all those tons of marijuana. Where in the heck are you going to put them?" Deac asked.

In other parts of the country with as Florida with its easily accessible coastline, seizure of ton quantities of marijuana are fairly common and the marijuana always is photographed, sampled, and burned, according to prosecutor Blake.

"I'm not sure yet what all the implications of the ruling are," Blake said. "Under ordinary circumstances I would expect to introduce testimony on the amount seized. If I can't, it changes the appearance of the case."