CAPE CANAVERAL, JAN. 13 -- The Defense Department and NASA will jointly develop a giant new unmanned super booster for the 1990s, but the military will pay for the project under a plan signed today by President Reagan.

Called the "advanced launch system," or ALS, the proposed new rocket represents another step in a buildup of the nation's military space program prompted in part by the 1986 Challenger disaster.

In a report to Congress on the status of the ALS program, Reagan approved creation of a joint National Aeronautics and Space Administration-Defense Department management structure for the ALS project, which calls for an operational rocket "no later than 1998."

As envisioned, the ALS rocket would be based on new technology and capable of carrying more than 100,000 pounds of payload into low orbit.

A major goal of the program is to reduce cost of launching a pound of cargo from about $3,600 to $400. NASA's manned space shuttle and the Air Force's new Titan 4 rocket can safely carry fewer than 40,000 pounds of cargo into low orbit in a launch.

The Air Force has approval for a $6 billion program to build 23 shuttle-class Titan 4 rockets along with more than two dozen smaller Delta 2 launchers in a major military space buildup designed to ensure access to space for high-priority military payloads regardless of the shuttle program.

The first Titan 4 was delivered to Cape Canaveral Air Force Station Tuesday, and its first flight is scheduled later this year.

The ALS rocket would be capable of carrying more than twice the cargo of a Titan 4, and the Air Force would serve as program manager, with NASA as deputy program manager.

On July 10, ALS "concept definition" contracts valued at $5 million each were awarded to seven aerospace contractors to explore the technology requirements of the proposed rocket.

In June, the field will be narrowed to two companies and if all goes well, one will win a development contract in July 1989.