''It's disappointing,'' Maj. Frank M. DeArmand, a would-be Air Force astronaut, said in an interview. ''We all had the excitement and expectation of flying on the shuttle. But I'm not bitter. It was the right decision.'' Michael Cassutt, the author of ''Who's Who in Space,'' an expert on the Defense Department's shuttle program, said relations between the military and the space agency had been strained for some time and seemed beyond repair.

The two ''have been separated for years, but the final papers are now showing up,'' he said, adding, ''The divorce seems to be final.'' Challenger: The Final Blow

The military's disenchantment with the shuttle began in the early 1980's, when poor shuttle performance, budget cuts and repeated delays caused only a fraction of proposed flights to get off the ground. The Challenger disaster of January 1986, which killed seven astronauts and grounded the shuttle program for 32 months, dealt the final blow, giving the Defense Department a reason to cut ties to the space agency's shuttles and an opportunity to acquire many more unmanned rockets.

In the very beginning, the Pentagon was excited by the prospect of manned spaceflight. In the early 1960's, it studied ways to send military astronauts aloft in various types of spaceships, including winged ones.

When NASA lobbied the White House for the current shuttle in the late 1960's and early 1970's, the Air Force grudgingly joined the project, attracted by the idea but wary of yielding its pre-eminence in space to civilians. To White House budget planners, the costly civilian shuttle program made economic sense only if it launched all American space payloads.

In the late 1970's, amid great secrecy, the military began building a coast-to-coast organization to take advantage of the civilian shuttles to launch top-secret payloads like spy and early-warning satellites.

In 1979, the Air Force Space Division in Los Angeles founded the Manned Spaceflight Engineer Program, an elite corps of military astronauts that was to specialize in deploying top-secret payloads. Mr. Cassutt said corps members were told they would fly in space at least once. The secret program, he added, eventually trained 32 engineers and had an annual budget of about $4 million.