For every three drug smugglers the U.S. Coast Guard caught recently in its war on dope, more than one member of the agency's main anti-smuggling units was punished for drug violations, a study for the San Jose Mercury News has found.

Members of the units - which are based throughout the country from San Francisco to Miami - were disciplined 428 times for drug offenses in 1987 and 1988, according to the 16-month study by the Coast Guard in response to a Freedom of Information Act request by the San Jose newspaper.During the same two-year period, the Coast Guard arrested or helped other law enforcement agencies arrest 1,099 people for drug offenses. That means one person assigned to the agency's"front line" in law enforcement, as one official described the units, was disciplined for every 2.6 civilians the agency busted for drugs.

Cocaine was involved in 48 percent of the punishment cases, only slightly less often than marijuana. A handful of other cases involved morphine, PCP and methamphetamine, or "speed."

It was hard to tell from the sketchy documents provided by the Coast Guard where the offenses occurred in many cases, but at least 32 of the disciplined employees appeared to have been stationed in or near San Francisco, Alameda, Calif., and Monterey, Calif. The South Florida area had the biggest share of punished personnel - at least 73.

Although the study showed that one member of the units was punished for drugs every 41 hours, on average, Coast Guard officials said it would be wrong to conclude that drugs have seriously undermined the agency.

The study merely proves drugs are used in all levels of society, they said, and that the Coast Guard - the country's main military agency involved in drug interdiction - is serious about punishing drug abusers in its ranks.

''We would be naive to think that we can have a corps of 38,000 active duty Coast Guard men and women and not have some of those incidents occur," said Cmdr. John McElwain, the agency's principal spokesman. "We reflect society."

Nevertheless, the study's results worried Kevin Zeese, vice president and general counsel of the Washington-based Drug Policy Foundation, which has objected to the military's growing drug interdiction responsibilities.

If Coast Guard officials are using drugs, Mr. Zeese said, they might become vulnerable to dope dealers who offer them bribes in exchange for tips about Coast Guard anti-drug operations. "Military guys are paid so little," Mr. Zeese said, that some of them might become corrupted.

''That is a great concern that we have," conceded Jim Simpson, spokesman for the commandant, Adm. Paul A. Yost Jr. "That is why we have such a hard-nosed urinalysis program, because we are aware of our vulnerability as a law enforcement agency."

He pointed out that 10.3 percent of Coast Guard members tested positive for drugs in 1984, but that number dropped to less than 1 percent in 1989. All personnel take such tests.

What's more, Mr. Simpson said, comparing the number of Coast Guard members disciplined for drugs with the number of civilians the agency busts for dope is "ridiculous" because "You're talking about arrest of smugglers who are bringing in dope by the ton, vs. a guy who gets caught because he went to a party and smoked a joint and we caught him."