President Reagan exempted his "Star Wars" missile defense program and the 2.1 million people now in military uniforms from the 4.9 percent spending cuts to be imposed to meet requirements of the Gramm-Rudman-Hollings antideficit legislation, Defense Department officials said yesterday.

Pentagon comptroller Robert W. Helm said Congress has already cut so deeply into the missile defense effort, known formally as the Strategic Defense Initiative, that Reagan feared further reductions would jeopardize future experiments. Helm cited an effort to develop a rapid-fire "rail gun" for shooting down enemy missiles as one program that would have suffered from another cut.

Congress has approved $2.76 billion for SDI in fiscal 1986, considerably less than the Pentagon request. The proposed Gramm-Rudman-Hollings reduction of 4.9 percent in the 1986 budget would have pared another $135.2 million. By completely shielding the program from any cuts, the administration served notice that it would go all-out to protect SDI.

Pentagon officials said that if the military personnel account was not shielded from the cuts, 280,000 uniformed personnel would have to be cut from the Army, Navy, Air Force and Marine Corps.

An administration official said at a White House briefing yesterday that the Pentagon might pad its future budget requests to spare SDI from cuts expected to be considerably deeper in coming years. "It's a matter of budget strategy," added the official, who could not be identified under the ground rules of the briefing. "It is not uncommon to ask for more than one absolutely must have."

Helm, asked about this statement at the Pentagon's briefing, labeled it "ridiculous and absurd."

Under the antideficit legislation, the Defense Department was given the option of shielding one item within a budget account -- such as aircraft procurement -- but other programs within that account would suffer deeper cuts to make up the difference. The department chose not to do this except in a few cases such as SDI, military personnel and certain fixed-price contracts, Helm said, for fear it would cause turbulence throughout the Defense Department and military contracting centers around the country.

Except for a short list of programs, all military accounts will be cut by 4.9 percent. No weapons will be canceled, Pentagon officials said, but project managers will have to find a way to keep existing programs going with fewer dollars.

Helm said the military services will have to buy less ammunition and try to stay ready for combat with less training because of the cuts. "You're not going to be as ready tomorrow as you would like to be," the comptroller added.

"It's an unattractive way to go," Helm said of the belt-tightening. "The practical effect is that we have now deliberately underfunded the program approved just two months ago" by Congress.

The Pentagon reduced budget authority for fiscal 1986 by $13.3 billion to achieve a $5.1 billion savings in military spending. The biggest cut was in the procurement of weaponry -- $6.6 billion in budget authority and $864 million in spending -- while operations and maintenance funds were reduced by $3.9 billion in budget authority to save $2.9 billion in spending.

The Navy emerged as a big winner. Research and development funds for its A6F bomber, F14 fighter, AV8B jump jet and EA6B electronic jamming plane all escaped cuts. Helm said this was because the Navy had signed fixed-price contracts that Defense Secretary Caspar W. Weinberger did not want to jeopardize by amending them.

By exempting the Star Wars program within the defense agencies' budget account, the Pentagon will have to cut twice as much from other organizations funded within the same account, including the Defense Mapping Agency, Defense Advanced Research Projects Agency and National Security Agency.