The Air Force conceded yesterday that its proposed MX missile system would have a "significant" environmental impact in the western sites where it would be deployed, but said all effects were manageable and that the system should be built.

There was quick desagreement with the 1,900-page environmental impact statement from representatives of 13 environmental organizations, who said the MX meant "unparalleled environmental destruction." In a letter, they asked President-elect Ronald Reagan "to give serious consideration to canceling the MX program."

The Air Force picked the tiny towns of Coyote Spring, Nev., and Milford, Utah, as first choices for air bases of 13,000 to 17,000 military personnel each. Impacts in those areas would be "not negligible but manageable," Air Force Undersecretary Antonia Handler Chayes told a news conference.

These bases would maintain and control the 200 missiles as they moved on flatbed trucks in a giant shell game among 4,600 underground shelters linked by roads over 8,500 square miles of flat desert land. The report listed eight alternative sites, six of them also in Nevada and Utah, which could be chosen if the two first choices are somehow ruled out.

The seventh alternative would put one base in Clovis, N.M., and another in Dalhart, Tex., while the eighth, the "split-basing alternative," would use the Clovis, N.M., and Coyote Spring sites.

Chayes said the two first-choice sites were better prepared to absorb the inevitable impacts of sudden population growth than the other locations.In addition, she said, much of the necessary land would have to be purchased in Texas and New Mexico but is already owned by the government in Utah and Nevada.

The $17 million study defended MX (for "missile experimental") as an integral part of the so-called "triad" of land, sea and air defenses, but Reagan in his preelection debate with Rep. John Anderson called the plan "fantastic" and said, "We need the missile, I think . . . but I am not in favor of the plan that is so costly." Chayes stuck with the official $34 billion cost estimate, although other estimates have ranged as high as $108 billion.

Insiders say the future of the project is not yet secure, but Chayes said the Air Force is continuing to plan "as President Carter chose to do it, with alternatives so that [the new administration] can choose."

The areas selected are so sparsely settled that only 10 buildings would have to be relocated in Nevada and none in Utah, the report said. During MX construction from 1982 to 1990, about 85,000 people would go into the area, and 31,000 would stay for good. That would mean 24,600 new jobs in the peak 1986 construction year for Coyote Spring, which is merely an intersection now, and 13,600 for Milford, Utah, which now has 1,217 inhabitants.

"Very significant growth problems in the rural counties are likely," the study said. The states would have to absorb $1.2 billion in 1986, the peak year, along with "significant increases in local land values . . . temporary shortages of some goods, services and skilled construction labor." Housing will be "a major problem" and shortages of doctors, dentists and nurses "could become critical" in the short term, while stress on the rural culture "will . . . be overwhelming."

"While the impacts may appear severe when viewed from the perspective of a little-developed area, when viewed from a national perspective . . . they are not that large," Chayes said. The study outlined ways to mitigate all the impacts, including phases hiring, financial and technical aid to local planners, and incentives to keep construction workers from descending on local townsfolk. There is "a great deal of support, and it is increasing" from businesses and farm families, although ranchers and miners had "expressed concern," Chayes said.

The nine-volume report said that 160,000 acres of desert vegetation in Nevada and Utah would be disturbed to contruct the 8,500 miles of roads and the shelters, or 10,000 acres more tnan if MX went to Texas and New Mexico.

Water rights will be purchased or leased, or water will be piped in, Chayes said. "We recognize the importance of literally every drop," she said.

The study evaluated 36 environmental issues, including impacts on the sage grouse ("significant"), bighorn sheep ("low") and other animals. Air quality could suffer "significant short-term impacts" from construction dust, but reclamation efforts using nonwater methods would minimize it, the report said. It added that MX deployment could slow an expected area boom in mineral mining because it "would have to complete with MX for labor, materials and equipment."

Rep. Jim Santini (D-Nev.) immediately condemned the report as glossing over energy, water and community problems. "If private industry had prepared a document as inadequate," he said, "it would be soundly rejected." He called for a congressional investigation of the study.

The environmental groups said the study "leaves no doubt that the MX system would permanently alter the human and natural environment of a large area" and might not even be an effective defense weapon.

Chayes said that "the Defense Department does not regard 'no action' as a serious alternative." She said the fourth and final environmental impact statement is due next summer. The four drafts will cost a total of about $24 million, she said.