Pentagon leaders, bracing for budget cuts of up to 12 percent in what they planned to spend on military programs over the next five years, said yesterday they expect to reduce troop levels by about 5 percent and kill several major weapons programs to meet the financial constraints.

Defense Department officials have warned the chiefs of military services and Pentagon agencies to prepare for cutbacks in planned program expansions, including President Reagan's Strategic Defense Initiative, commonly called the "Star Wars" missile defense program.

Pentagon officials said they have ordered the military services and agencies to begin planning for cuts far beyond the limits set by Congress and the White House in the fiscal 1989 budget.

"We've told them we're looking at a five-year drought as opposed to a one-year freak," Deputy Defense Secretary William H. Taft IV told a group of reporters yesterday.

The 12 percent cutbacks most likely will mean more reductions in the Pentagon's plans to expand existing programs and start new ones, rather than in actual cuts to current programs. Taft said the Pentagon had expected 2 percent in real growth for each of the next four or five years. The anticipated cutbacks mark a reversal from the administration's early years, when the Pentagon budget ballooned.

Defense Secretary Frank C. Carlucci already has ordered the services and agencies to draft plans for slashing $33 billion out of the Pentagon's fiscal 1989 budget to achieve cuts approved in a deficit-reduction compromise between the Reagan administration and Congress on Nov. 20. That will mean a cut of about 10 percent from what the Pentagon originally sought in its 1989 budget authorization.

The decision on the fiscal 1989 budget was made even before Congress approved and Reagan signed the fiscal 1988 authorization bill last week, complicating Carlucci's orders, which went out Nov. 23, the day he took over as defense secretary.

Congress has approved a $296 billion authorization for military programs in fiscal 1988. Under the agreement reached in the congressional-White House budget summit, the Pentagon will submit a budget of $299 billion to Congress next spring -- significantly lower than the $332 billion former Defense Secretary Caspar W. Weinberger had planned to present to Congress.

And, although the Pentagon does not yet have to produce exact figures for 1990-94 -- the remainder of its five-year-plan -- Carlucci has warned officials against making the 1989 reductions without considering their implications in future years.

The Pentagon's top officials say that they have told the services that some personnel cuts will be "inevitable" to meet the budget demands.

"We would rather go with a somewhat smaller force if for the same price we would have a larger, but less ready and capable force," Taft said.

Taft said Army leaders have expressed the strongest resistance to imposing force reductions, complaining that the Army already is at its lowest troop levels since the Korean War.

Carlucci has ordered Pentagon leaders to eliminate programs rather than stretch them out to inefficient production levels over the next few years. Defense Department officials said these demands will jeopardize plans to buy improved versions of some aircraft, new weapons systems and perhaps some Navy ships, including plans for two new aircraft carriers.

Taft said the services have been encouraged to make bigger cuts in research and development programs than in ongoing procurement programs, which he said already have been cut significantly in recent years.