FOR THE LAST 18 months the State Department has been telling the world that the Soviets have dropped a deadly biochemical agent nicknamed "yellow rain" on resistance fighters in Southeast Asia and Afghanistan. What if the clouds of ochre dust and the toxic fungus that have been identified were both natural phenomena, locally grown and distributed by the tropical winds?

If possible, this would certainly undermine the administration's confident assertion that the Kremlin has been manufacturing "yellow rain" containing a poisonous fungus and spraying it from aircraft and helicopters in contravention of international treaties.

Such doubts may seem a little absurd after the heap of eye-witness accounts of the mysterious yellow clouds, human blood samples showing the presence of fungus poison and hundreds of scraps of vegetation dotted with yellow spots.

That circumstantial evidence cannot be dismissed. But the work of an Australian government scientist named Hugh Crone, studying the issue for the Australian Department of Defense, has raised questions about some of the State Department's evidence. He analyzed samples of "yellow rain" collected by the Australian Department of Foreign Affairs, with the help of the United States, and concluded that "the items were fakes." Crone said they seemed to have been deliberately made up from local pollen and fungi spores.

Other scientists have studied similar samples without raising such a provocative conclusion. In his research, Crone found among the pollen grains traces of a poisonous fungi, but nothing, he said, which could be considered harmful to humans or "militarily effective." Indeed, some of the pollen samples resembled the pollen produced by local rainforest trees.

Crone speculated that someone had collected the pollen, which had somehow become contaminated with fungi and which was then deliberately applied to leaves and pebbles. "Since the examples are obvious fakes," wrote Crone, "they convey no information at all as to the veracity . . . of the reports of the chemical attacks. The reasons for their fabrication can only be guessed at; monetary gain, desire to ingratiate oneself with authority, or as a disinformation campaign."

For no clear reason, the Australian government sat on the Crone report for six months, releasing it last week after its contents had been described in the London Observer. Paul O'Sullivan, a political officer at the Australian embassy in Washington, said he was concerned that Crone's results might be taken out of context. "It's a neutral analysis," he said, "but it certainly does open the question: What do we know about the pollen?"

The State Department official responsible for "yellow rain," Gary Crocker, was reluctant to discuss the report. Even to mention it, he said, was "talking out of school."

Crocker acknowledged that "we don't fully understand it (the pollen contact of the samples) yet." Scientists at the U.S. Army's chemical systems laboratory, which has done research on yellow rain for the state department, have been investigating the pollen question since last October.

The Crone findings do not prove or disprove anything. The samples Crone studied came from one incident on the Thai border, and do not necessarily have wider relevance.

His findings are, however, politically significant. The suggestion that the samples were fakes reopens the question of whether "yellow rain" could, in fact, be a natural phenomenon, such as large quantities of pollen borne by the winds, not dumped by the Soviets or their proxies. As Sherlock Holmes might have put it: Is this a case of the windborne pollen that was not borne on the wind?

In fact, Holmes would have been clever enough to decline this case. Too much of the relevant information is unknown or unknowable. The debate over whether the Soviets are violating the 1925 Geneva Protocol and the 1972 biological weapons convention in Afghanistan and Indochina is still a political dispute, albeit one involving scientific evidence. Unfortunately, that evidence will probably never be conclusive. And there certainly is circumstantial evidence supporting the theory that the Soviets are using biochemical weapons.

The problem with the State Department's "yellow rain" case -- that the toxic substance has been sprayed on dissident H'Mong tribesmen in Laos, on the forces resisting the Vietnamese invasion of Kampuchea, and, more recently, on the mujahidin in Afghanistan -- has always been the lack of a conclusive smoking gun.

No one has found a rocket or an empty shell used to deliver "yellow rain," nor have there been any reliable autopsies of bodies of people who have obviously been killed by "yellow rain." The only man-made exhibits so far are two Soviet gas masks from Afghanistan, which, when analyzed in American laboratories, were found to be contaminated with the poisonous ingredient of "yellow rain" known as trichothecene mycotoxin.

In the scientific community there has always been a lingering doubt about the true origins of the yellow substance because of the gap between the bold assertions by the State Department about "compelling" proof and the uncertain scientific evidence.

From the beginning, the State Department has tended to exaggerate the scientific evience. Alexander M. Haig Jr., as secretary of state, fired the first salvo in a speech in Berlin in September 1981. "We now have physical evidence from Southeast Asia, which has been analyzed and found to contain abnormally high levels of three potent mycotoxins -- poisonous substances not indigenous to the region." His "evidence," it turned out, was a single leaf and a stem.

A subsequent search of the scientific literature by R.D. Caldwell of the department of plant pathology at the University of Wisconsin revealed that the particular fungus, fusarium, which produces the mycotoxin found in the analyses had been described in Vietnam in the 1930s.

In November last year, Haig's successor at the State Department, George Shultz, signed a more detailed 12-page special report on chemical warfare in Southeast Asia and Afghanistan that was based on additional evidence. Shultz concluded, "Chemical and toxin weapons are bing used today in Laos, Kampuchea and Afghanistan by the Soviet Union and its allies."

It now seems beyond dispute that the Soviets have used chemical agents in those countries -- chemicals like tear gas and "mace" that can debilitate humans. The crucial political issue is whether the Soviets have strayed across the line defined by the 1925 and 1972 agreements that forbid the use of more toxic chemical and biological agents.

The U.S. government concludes that the Soviets have crossed that line. But others besides the Australians decline to go that far. The Canadian government has published more cautious findings, concluding that toxic agents "possibly mycotoxins," have been used in Laos, Cambodia and Thailand.

The State Department's collection and presentation of its evidence has always been intended to prove that the Soviets are using mycotoxins, and not to explore the possibility of disproving the counter hypothesis that the pollen and the fungi occurs naturally.

Crocker of the State Department says the counter hypothesis is "just not interesting" in the face of the wealth of eye-witness accounts of yellow clouds.

He says that the samples do contain pollen and that the Russians have managed to use commercially collected pollen as the carrying agent for the mycotoxins. Crocker says there is evidence, albeit inconclusive, to suggest the Russians have filtered the pollen grains to a special size that is easily ingested or inhaled and then retained in the body long enough to disperse its poisons. Would a serious detective -- Holmes, for instance -- go so far to gather evidence suiting only one theory of the crime?

According to Crocks are vioer, the Australian "yellow rain" samples on leaves and pebbles came from an incident in eastern Thailand, 10 kilometers from the Kampuchean border, on Feb. 19, 1982. The Shultz report says that on that day "a sample of contaminated vegetation was obtained following spraying by a Vietnamese aircraft." Crocker says "yellow rain" hit six villages, and "just about everyone in the world got samples" -- the Australians, the British, the French, the Canadians and the Americans.

The Australians, according to the Crone report, found only harmless traces of mycotoxins. The Americans, according to Crocker, had similar results; there was no sign of military quantities of mycotoxins. The French and British have come to similar conclusions, an official said.

A Canadian team was able to do its own epidemiological study in the village soon after the attack. It found an "uncommon level of illness" among some of the villagers. Coughing, headache, dizziness, loss of appetite, dryness in the throat, itching, and fatigue were the "most prevalent symptoms" of the 33 villagers interviewed, 21 of whom were ill, though none required major medical treatment.

The report adds, "The occurrence of contact dermatitis suggests an allergic response. The fact that all affected experienced a non- productive, dry cough . . . tends to support this hypothesis." The Canadians said it was possible the allergic reactions were caused by natural pollens, but said they could draw no conclusion on the cause of the illness they observed.

Crocker says the motive for the attack is a mystery. The yellow part of the "yellow rain" was indeed pollen, but it does not seem to have been toxic to any significant degree. "This is probably the most confusing of all the stories (about yellow rain) I have seen over the years," says Crocker. "At first we thought maybe this was a spoof because we couldn't make any sense of why they (the Vietnamese, or whoever was piloting the plane) came over Thailand. Maybe the Soviets thought people would collect the pollen and it would discredit the U.S. case . . . I just don't know why they used sub-lethal doses."

The Feb. 19 incident raises all sorts of questions. Was the aircraft in fact a Vietnamese aircraft, as the State Department report asserts? The Canadian report says the plane had no markings. Did the plane villagers saw actually dump the yellow dust? Could the pollen have been produced locally? Did it come in on the wind?

Such questions are unlikely ever to be answered. The event took place more than a year ago, memories fade, and the material evidence is no longer there. In any case, in order to postulate a natural phenomenon one has to stretch the imagination: huge quantities of pollen, suddenly released by plants or trees, forming a cloud that subsequently breaks up and deposits yellow dust on leaves and pebbles.

If this is proposed as a possible explanation for the whole "yellow rain" saga, can windborne pollen stick to leaves and pebbles and than attract passing windborne spores of fungus which then produce mycotoxins that are somehow ingested by local inhabitants of these regions? Has this happened in Laos and Kampuchea before? Is there any evidence of naturally occurring mycotoxin poisoning?

These are some of the questions raised by the Australian report. The science of pollen identification is murky. But the Australian questions seem worth pursuing, particularly if, as Crone charged, there were grounds to consider the samples from Thailand "fakes."

If the State Department decides to pursue the indigenous pollen theory of "yellow rain," it could do worse than to begin with an indigenous report.

The Australians are not the only ones to report pollen findings. Last spring a group of Thai scientists at Mahidol University analyzed yellow spot samples collected from the Thiland border eight kilometers from Kampuchea. The samples consisted of pollen of the genus Compositae, of the daisy family, plus some "fungal elements." A mycotoxin was isolatedvio from two of the 22 yellow spots, and the crude extract of this fungus killed experimental mice. "Therefore," concludes the Thai report," the possible producers of trichothecene mycotoxins existing in Thailand were either in nature or mixed together with pollen or unknown sources.