President Reagan has decided to appoint Alton G. Keel Jr., who served as executive director of the Rogers Commission, as acting deputy director of the National Security Council while the current deputy, Donald R. Fortier, is ill, White House officials said yesterday.

An announcement of the appointment is expected today, officials said.

Fortier, who has earned a reputation as an astute political and congressional analyst under national security affairs adviser John M. Poindexter, has been seriously ill since May.

Keel, 42, came to the administration in 1981 as Air Force assistant secretary for research, development and engineering. He later served as associate director of the Office of Management and Budget for national security and international affairs, becoming a key adviser to then-Director David A. Stockman.

In that capacity, Keel played a key role in defense budget and policy decisions. Keel also was instrumental in guiding to passage the Export Administration Act, and was later considered as one of two finalists for the jobs of budget director and Air Force secretary.

After the Jan. 28 explosion of the space shuttle Challenger, Keel was named executive director of the presidential commission headed by William P. Rogers investigating the accident, and was credited with helping produce the report on time under intense pressure and after extensive investigation.

Keel previously served on the Senate Armed Services Committee staff under Chairman John G. Tower (R-Tex.) and has close ties to key foreign policy and national security panels on Capitol Hill.

Poindexter has told associates that he has been hampered by Fortier's absence. Some White House officials view Keel's appointment as an effort to respond to this on a temporary basis by bringing in an experienced aide who can quickly begin to deal with Congress and others on national security issues.

Fortier, 39, is credited with playing a key role in the administration's effort to challenge Soviet aggression by supporting "freedom fighters" in such places as Nicaragua and Afghanistan, a policy some have called the "Reagan doctrine."

Fortier also helped the administration engineer a compromise last year that won Reagan $27 million in humanitarian aid to the Nicaraguan contras.

White House officials said Keel is expected to continue Fortier's major efforts to achieve bipartisan consensus on critical foreign policy issues. Fortier had previously worked for House Foreign Affairs subcommittee Chairman Lee H. Hamilton (D-Ind.), and in 1981 became deputy director of the State Department policy-planning staff.