The State Department said yesterday that the new "bee droppings" theory of "yellow rain" chemical warfare in Asia is false and has been dismissed by government scientists.

The United States has accused the Soviet Union of making a deadly chemical agent and using it in Afghanistan, as well as giving it to its allies in Laos and Cambodia. Thousands have been killed by the poison in recent years, the United States has charged.

But a panel of scientists Tuesday said that "yellow rain" samples cited as evidence by the government are almost certainly pollen-filled bee feces and that a poi- son--tricothecene mycotoxin--found in some of the samples could have either a natural or manmade origin.

State Department spokesman Alan Romberg said yesterday that the bee-feces theory does not take into account a large mass of other evidence, including eyewitness reports of planes dropping yellow clouds and other reports by victims, medical workers, journalists, defectors and government officials.

Romberg said toxins have been found in bodies of alleged chemical warfare victims and in the blood and urine of people who claim to have been in chemical attacks.

He also said that the toxin samples found on leaves and other materials are too large and too narrowly spread geographically in war zones to be explained as bee droppings.

"The hypothesis that yellow rain--tricothecene mycotoxin--may be a natural phenomenom has in fact been exhaustively studied and subsequently rejected, by responsible and qualified scientists in and out of government," Romberg said.

In a report to the American Association for the Advancement of Science in Detroit Tuesday, five scientists said they believe the yellow spots are droppings from the giant honeybee of Asia, called apis Dorsata. They said bees naturally store large amounts of pollen in their bodies and excrete it in flight.

They acknowledged that their theory does not explain why toxins are present in some samples of the pollen. One possibility, they said, is that chemical warfare toxin landed on the bee spots and that the U.S. government is right. But it is also possible, they said, that natural fungi grew in the bee spots, producing the mycotoxins and causing the illness of some refugees.

Harvard biologist Matthew Meselson, an expert on chemical warfare and one of the five panelists, responded to the State Department yesterday by saying that the government should bring the panelists and the government scientists together in a non-political forum.

He said a paper outlining areas of agreement and disagreement and methods to resolve differences would greatly help the government's position and credibility.

As it stands now, Meselson said, the government's position that the presence of mycotoxins is due to chemical warfare attacks "lacks adequate controls . . . . We are not stating that the State Department must be wrong. We are stating that there is serious room for doubt."

The State Department yesterday raised several direct objections to the "bee droppings" theory:

* "One sample residue droplet in which the toxin was present . . . weighed 300 milligrams a hundredth of an ounce --certainly more than a bee could drop."

* "The level of toxin causing immediate, and often fatal, effects in humans is certainly enough to kill a bee . . . a bee could not survive to excrete the toxin."

* Three samples--one taken from water in Southeast Asia and two taken from Soviet gas masks in Afghanistan--had mycotoxin poisons but no pollen.

* The occurrences of yellow rain have been limited to war zones, but if the bee theory is right, other people would be affected throughout the region. No such phenomenon has been observed.