Skirmishes between government agencies are nothing new, but the State Department and the U.S. Customs Service have given new meaning to the administration's war on drugs.

In internal correspondence, Customs Commissioner William von Raab has charged that the State Department is "soft on drugs." In turn, a State Department official has charged that von Raab is pursuing a policy akin to "branding" individuals accused of drug offenses.

At issue is what should happen to the passports of Americans who are apprehended at border checkpoints smuggling drugs. Because of a smuggler glut in the legal system, many of the accused, especially those carrying smaller amounts, are allowed to plead guilty and pay a fine of $100 to $150.

The Customs Service would like to stamp the passports of violators so that if they leave and enter the country again, Customs officials will have a handy marker of past drug offenses.

But the State Department, the agency in charge of U.S. passports, has refused to go along, saying that such stamping might interfere with "the integrity of the document."

According to an exchange of letters obtained by The Washington Post, von Raab has been trying for 16 months to persuade Joan M. Clark, assistant secretary of state for consular affairs, to go along with his proposal.

"The stamping of passports will serve two purposes," von Raab said in an Aug. 22, 1986, letter. "It will alert Customs officers to possible drug smugglers, and it will deter individuals from smuggling drugs into this country.

"Customs officers presently examine passports to determine if an individual has recently traveled in a drug-source country. A stamped passport will indicate to a Customs officer that the passport holder has previously attempted to smuggle drugs and, therefore, a more thorough examination may be appropriate," he said.

"An individual with a stamped passport will quickly learn that he will be subject to a thorough examination upon entry into the United States; and, consequently, he may decide his chances of getting caught are too great to attempt to smuggle drugs," von Raab said.

In a Nov. 4, 1987, reply, Clark said the State Department could not go along with von Raab's request. "I trust you realize that my reluctance to stamp passports has nothing to do with the department's commitment to eradicating the drug problem in the United States. Rather, we are concerned with maintaining the integrity of the document," she said.

Von Raab escalated his campaign on Dec. 9 in another letter to Clark in which he said he was disappointed in her decision and charged that the State Department is "soft on drugs."

He said he supported a "zero tolerance" approach to drugs. "That is, we will not tolerate any drugs from anyone, anytime . . . . I continue to be frustrated with the inaction that is characterizing the State Department on drug smuggling.

"Why not seize passports of drug smugglers and make them reapply for new ones or to reclaim the seized one? Why not stamp the passports indicating they smuggled drugs? These actions do not seem serious when considering an individual was caught with drugs," von Raab said.

"We have an opportunity to have a real impact on this drug problem that is devastating our country. Do not let the bureaucrats persuade you to 'do nothing' or let the process neuter every good idea," von Raab said.

Asked for comment on the letters, von Raab said through a spokesman that he found the State Department's stance "to be a disappointing bureaucratic response to a serious problem that is threatening our nation's health and security." He refused to elaborate.

Clark would not comment.

But Phyllis Bucsko, director of the policy and coordination staff at the State Department's Bureau of Consular Affairs, said, "If people are illegally carrying drugs, then they ought to be prosecuted under the law. Either it's illegal or it isn't illegal.

"Our conclusion is that the passport is a travel document. We would be violating constitutional rights by stamping them. It's somewhat akin to branding," she said.

Bucsko said the State Department is concerned that passports of individuals who have not gone through the U.S. legal system would be stamped. Customs sources responded that the individuals in question would be caught at a border with drugs in their possession and would enter guilty pleas when paying fines.

"There has also been a suggestion," Bucsko added, "that we stamp the passports of persons who have been tried and convicted and sentenced for drugs. But the price of violating the law does not include having your passport stamped for the rest of your life -- once you've paid your dues to the legal system. If the courts want to tell us to do this, that's one thing. But for us to decide to do this does not seem reasonable.

"No one at the State Department is soft on drugs, but this would put {people whose passports are stamped} at great risk in their travels, especially in any of the Middle Eastern countries, when they haven't even gone through the legal system in the United States."

Bucsko complained that Customs has failed to respond to a State Department request for a legal opinion showing that document stamping would be legal, but Customs sources said von Raab had requested the State Department to prepare the legal opinion because it administers the laws dealing with passports.

The Customs sources warn that von Raab is not ready to concede defeat. He warned in his last letter, "I intend to move forward and hope you will join me."

Associates say he is considering ordering employes to seize the passports of drug smugglers caught at border stations. The seized passports would then be shipped to the State Department for disposition.