Andrew J. Stofan, the head of NASA's space station program, will retire on April 1, the agency announced yesterday. His successor has not been selected.

Stofan, 53, who started with the National Aeronautics and Space Administration 30 years ago as a research engineer, has shepherded the space station through a troubled period.

In June 1986, in the turmoil that followed the Jan. 28 Challenger shuttle disaster, he was appointed associate administrator for space station.

He has supervised a major management reorganization and an accounting review that revealed the costs of the station had been seriously underestimated, prompting the administration to split the station into two phases and scale it back.

Eight major contracts have been awarded and work has begun.

Stofan has also been outspoken in the continuing fight to preserve station funding in the budget process in Congress, most recently criticizing Congress, NASA and President Reagan for a lack of leadership.

Congress approved $425 million in start-up funds for the controversial station in the fiscal 1988 budget, instead of the $767 million the administration requested, and the station faces more money problems this year.

Dismissing rumors that Stofan had been forced out, spokesman Mark Hess said Stofan had always planned to leave after accomplishing certain goals. Stofan said in a statement, "I've accomplished everything I set out to do when I came here . . . . The program is on track now."