The enemy is vanquished, but the war goes on.

In 1977, the world recorded its last natural case of smallpox. In 1979, a global commission declared the once-rampant killer eradicated. In 1980, a World Health Organization conference recommended discontinuation of routine smallpox vaccinations. By last year, every nation except Albania was reported to have done so.

Supplies of the smallpox virus are known to exist in only two places: the federal Centers for Disease Control (CDC) in Atlanta and the Research Institute for Viral Preparations in Moscow, according to the American Public Health Association.

Yet, many countries, including the United States and the Soviet Union, persist in vaccinating their military forces against the disease, fearing that some day the smallpox virus may be used as a biological weapon.

But many health authorities inside and outside government contend that the military smallpox vaccinations should be stopped. They cite the small but real danger the immunization program poses to persons being vaccinated and to others who come in close contact with them.

Some health authorities are promoting the idea of a Soviet-American agreement to halt the smallpox vaccinations.

In a recent policy statement, the Defense Department informed the four military services that they "shall continue to immunize all military personnel against smallpox." This means shots for recruits -- about 320,000 each year in the Army, Navy, Air Force and Marines.

In addition, military health officials are drawing up a plan for vaccinating National Guard and reserve recruits and reimmunization of the nation's 2.1 million active-duty personnel.

A spokesman for the Defense Personnel Support Center in Philadelphia said that in 1983, the smallpox vaccine and an antidote for complications from immunization cost the government about $378,000. This does not include the cost of administering the shots.

"The fundamental rationale is that other armies use smallpox vaccination," said Dr. Jarrett Clinton, a deputy assistant secretary of defense. "Therefore . . . we think we should protect our people. The heart of the concern is that it might be used by some group as a biological weapon."

Some health experts question the vaccination program for several reasons:

* Smallpox inoculations commonly produce discomfort for the recipient as well as the rare but real possibility of serious health complications. Increasing numbers of recruits face their first vaccination, which carries the greatest risk.

Earlier risk estimates, based largely on the immunization of children, suggest that there are about 1 death and 74 complications -- ranging from encephalitis and nervous system damage to spreading of the inoculated virus to other parts of the body -- per million vaccinations, with far fewer problems with revaccinations, said CDC epidemiologist T. Stephen Jones. The risk to adults posed by the vaccine is unknown.

* The live virus used in smallpox shots, a weak relative of smallpox known as vaccinia, can be spread to unprotected civilians. Pentagon policy recommends limited contact between newly vaccinated personnel and the outside world.

The CDC reported last month that in January a 15-year-old Wisconsin girl developed a lip ulcer, arm lesions and an eye infection after applying compresses to the arm of a young National Guardsman who had just been immunized. In 1984, the CDC reported that a Louisiana woman was hospitalized after contact with her Marine boyfriend's smallpox shot. Similiar cases have been reported in Canada and Norway.

Although these illnesses were treatable, there is much greater "potential for serious or fatal complications" for exposed persons who have eczema or suffer from immune-system deficiencies because of cancer or other illnesses, the CDC warned.

* Critics say that smallpox is not an ideal agent for biological warfare and note that more potent alternatives are available.

The future availability and cost of smallpox vaccine is uncertain. Because routine smallpox vaccinations of civilians have stopped, the Defense Department is the only major American customer for the vaccine.

* For several months last year there was a shortage of an antidote needed in treating side effects of smallpox immunization.

The military services differ on the value of the vaccination program. Though the Army has always strongly supported it, there has been less support in recent years among Navy and Air Force health officials, sources say.

Both private and government health experts are quietly discussing the prospect of a U.S-Soviet accord to discontinue military smallpox inoculations and to work together instead in an international effort to immunize the world's children against other infectious diseases.

Dr. D.A. Henderson, dean of Johns Hopkins University's School of Hygiene and Public Health, said he spoke with World Health Organization Director-General H. Mahler in Geneva recently and "he thought it was a splendid idea."

"The Soviet Union and the U.S. are credited with playing a major role in eradicating smallpox," said Henderson, who headed WHO's eradication program. "They should take the next step and stop smallpox vaccination in the military and go forward and support a new global immunization effort.

"It might be a positive initiative which the Reagan administration could take with very little risk and the Russians would welcome" if President Reagan and Soviet leader Mikhail Gorbachev meet this year.

WHO efforts are now directed toward making immunization against other diseases available to all children by 1990. An estimated 5 million children die each year of diseases, such as polio, tetanus, measles and whooping cough, that can be prevented by vaccines. About two-thirds of the children in developing countries are not getting immunized. A Pan American Health Organization campaign to wipe out polio in the Western Hemisphere is to be announced soon.

"There is no question that the money the military spends on immunization programs for smallpox could be better spent on vaccines eliminating diseases of children, both in the U.S. and in developing countries," said Dr. Anthony Robbins, past president of the American Public Health Association. "It would be one small step for disarmament."

The idea of a U.S.-Soviet agreement to discontinue smallpox immunization among military troops is also being floated at the Department of Defense, sources said.

"We have eradicated a disease from the face of the Earth. What a great achievement of human cooperation. Yet, because we worry about each other, we immunize soldiers," one military health official said.

Both the United States and the Soviet Union signed a 1972 convention outlawing biological warfare.

In any case, experts question whether the smallpox virus would be a good biological weapon. "Those who know the field well say there are many far more lethal biological agents that might be used," said Hopkins' Henderson.

However, the Pentagon's Clinton said, "Although in the scale of things it's not considered terribly good, it nonetheless is a possibility."

The value of continuing the military's smallpox vaccinations has been questioned for years. The Armed Forces Epidemiological Board recommended in February 1984 that "public health considerations would dictate that routine smallpox vaccination be discontinued. However, . . . its continued use in military forces should be a command decision based on intelligence information and strategic needs."

After considerable debate, Dr. William Mayer, assistant secretary of defense for health affairs, signed a message to the services in March of this year saying: "The services shall continue to immunize all military personnel against smallpox. Appropriate procedures shall be implemented to minimize the potential for accidental secondary vaccinia infection of unvaccinated individuals."

Clinton said that Defense Department officials are not aware of any "serious problems" in reactions among vaccinated military personnel, but that records of problems among civilians might not come to their attention. He said a military group is working on new guidelines for the smallpox immunization program "so that it causes the least harm."

One group member, Col. Alfred K. Cheng, said that in the future better health records will be kept on the program "so we can weigh the risks and benefits."

Cheng emphasized that in his "personal opinion, I don't think it's a good idea" to immunize the military against smallpox. He added that "if somebody is going to spray that on us, we should protect the civilians as well."