While Friday's launch of Atlantis on a secret mission marks the Pentagon's return as a shuttle customer, the military is taking steps to sharply cut its reliance on the shuttle fleet.

The Atlantis lifted off from launch pad 39-B, one of two shuttle pads at NASA's Kennedy Space Center here.But the real activity in the next year will be down the beach at the Air Force's Eastern Space and Missile Center.

There, where the old Mercury capsules were launched during the early days of the space program, the Air Force is preparing to launch 16 expendable rockets by the end of September 1989. That includes a Delta 2 rocket and a Titan 4 rocket now sitting on launch pads. By 1991, the Air Force expects its launch rate for expendable rockets to be more than two dozen a year. That will include military payloads and commercial satellites for which the Air Force will provide launch facilities.

"We're going to be real busy," said Lt. Col. Ron Rand, spokesman for the missile center. There is concern, he said, that the anticipated launch rate will strain the resources of the launch facility. "We're going to be quadrupling, or even more, our launch rate with the same number of people," Rand said.

Air Force officials are concerned that they not fall into the same schedule pressures with their unmanned rockets that plagued NASA prior to the Challenger disaster.

"We're going to do it right," Rand said. "You don't have people aboard, but still you're launching a critical and valuable national resource."

The military payloads includes spy and communications satellites and "Star Wars" experiments.

The two rockets sitting on launch pads with military payloads were to have been launched in October. There were delays in updating the launch pads and placing the payloads aboard the rockets, Rand said. The launches now will be early next year, he said. The first major commercial launch under Air Force auspices - a satellite for India - is scheduled for April.

Even before the Challenger was destroyed in January 1986, the Air Force had been edgy about the policy of putting virtually all U.S. space cargoes aboard the shuttle. The service convinced Congress to allow it to buy 10 Titan 4 rockets as a backup to the shuttle. After the Challenger disaster, the Air Force ordered 13 more Titans, 20 medium-size Delta 2 rockets and 11 upgraded Atlas Centaurs, also medium-lift rockets.

The Pentagon now spends about twice as much on space programs as NASA, whose current budget is about $11 billion.

Despite its aggressive program to buy expendable rockets, the Air Force will continue to use the shuttle to deploy a backload of military cargoes that were specifically designed to fly only on the shuttle. The Pentagon will fly 10 more shuttles through 1993.

But the plans to operate a separate facility for military shuttle launches at Vandenberg Air Force Base in California have been shelved indefinitely and an unused launch facility, costing about $3 billion, is in mothballs.

Even with its accelerated schedule of rocket launches, some analysts say the Pentagon may not be able to significantly cut the operations costs of the launches. A recent report by the congressional Office of Technology Assessment concluded that "the number and diversity of payloads NASA and DOD (the Department of Defense) now plan to launch through the late 1990s do not meet the conditions necessary for dramatic cost reductions."