Typhoons, earthquakes, rivers of smoking lava. Through the years, natural adversity has been no stranger to the 4,300 persons who make their homes on this windy volcanic island 100 miles south of Tokyo.

Today, the island faces something that most inhabitants seem to consider a more serious threat -- a plan by the Japanese government to build a 6,500-foot runway for training U.S. military pilots.

The project has become a national priority for the government of Prime Minister Yasuhiro Nakasone. It would eliminate a major point of friction in military relations with the United States by creating a new place for pilots from the U.S. aircraft carrier Midway to practice night landings when the vessel is in port in Japan.

At present, they are using Atsugi Air Base just west of Tokyo. But long complaints about noise from the densely populated neighborhoods around the base have resulted in constraints on hours and frequency of the training.

The United States has taken no official position on the selection of Miyake Island, saying it is a Japanese decision and project. The subject is expected to come up when Defense Secretary Caspar W. Weinberger arrives in Tokyo Friday.

[Weinberger arrived Thursday at Chitose on Japan's northernmost main island of Hokkaido to watch tank exercises before inspecting an air base on Honshu and continuing on to Tokyo, Reuter reported.]

Eighty-five percent of the voting-age residents of the island have signed petitions opposing the plan. They are so incensed over it that they are doling out some rough justice to fellow islanders who favor it, shunning them and their children and boycotting their businesses.

"Since the gods made this land," said Tsugio Miura, a hotelier and president of a citizens' group that is fighting the plan, "this is the first time we have been divided."

It is a rare performance in Japan, where local politics usually is played out with the same poise and predictability that has kept the ruling Liberal Democratic Party in power for more than 30 years.

When a high-powered party delegation came here to lobby for acceptance of the project, opponents refused even to talk to them, saying that to do so would be the first step toward construction.

After years of surveys and studies, the Japanese government settled on Miyake Island as the only feasible spot in a land-poor country, even though the entire island is a national park -- it claims 220 species of birds -- and one end of the runway would be built on top of a volcanic crater, a 200-yard-wide hole left by an eruption in 1983.

The ruling party has appealed to patriotism and likelihood of prosperity. It has promised 23 development projects valued at about $45 million that would modernize facilities for the island's three main industries: agriculture, fishing and tourism. This, it is argued, would boost a flagging economy and stem an outflow of young people that has reduced the island's population by almost half since the 1950s.

The government argues that disruption would be tolerable, because training would occur less than one night in four and the jets' approach and departure would be over water. The rest of the time, the runway would be a new civilian airport, allowing commercial jets to fly tourists in from Tokyo for the first time.

But fishermen say the jets would scare off the fish. Hotelkeepers say the noise would scare off the tourists. Farmers say some of the island's best crop-growing land would be taken. Everybody worries about not getting sleep.

An American marine biologist who has lived here off and on for 35 years maintains that construction and operation would do extensive damage to rare plant and animal life on the six-mile-long island. The island consists of little more than the slopes of the volcano Ooyama.

The fight comes as local leaders in the town of Zushi, south of Tokyo, are waging a similar battle against Japanese government plans to build housing for U.S. military personnel on one of the Tokyo region's few remaining tracts of forest.

In both places, people say they are not anti-American, just pro-environment -- notwithstanding members of the Communist Party who have flown into Miyake Island to help out with the organizing. "Please convey to President Reagan that we are not opposing the U.S.-Japan security treaty," said Miyake's mayor, Haruo Terasawa. "We only want a place to be found where the inhabitants would not suffer."

Emotions have been hot since 1983, when the island's local legislative council approved the plan without consulting constituents and flew to Tokyo to inform Nakasone personally. When islanders found out, they angrily demanded a retraction -- and got it.

The battle continues. Noboru Kikuchi, an island restaurateur and councilman, says he is against the project but feels it is not reasonable to refuse to listen to what the government says. As a result, he has been tagged as "pro-base." Taxi drivers and hotel operators no longer bring guests to his place, he said, and business has dropped by half.

In one case talked about here, the body of an islander who died in Tokyo was not brought back for burial, as is the usual practice. The reason: the man's family favored the project and was afraid no one would show up for the funeral.

The government still talks of winning island "understanding." But it has legal authority to condemn the land and proceed without their approval. Mayor Terasawa says he worries that the island could become ungovernable if that happens.