Major weapons in President Reagan's defense buildup through the 1990s will cost $25 billion more than reported to Congress last year, but the projected cost increase is the lowest in recent years, the Pentagon announced yesterday.

Defense officials said the projected increase of less than 1 percent reflects the administration's efforts to control cost in weapons procurement, which is now under congressional scrutiny.

The Pentagon's projection focused on 84 major weapons whose costs were estimated in a September report to Congress to reach $725.6 billion in the 1990s. The same weapons are now expected to cost $750.7 billion, a 3.4 percent increase attributed mainly to larger quantities of arms and design improvements.

Using the Congressional Budget Office's measure, which excludes the impact of weapons added to the projections since last year, the cost increase is .87 percent. Over the past four years, cost-increase projections have ranged from 1 to 12.6 percent.

Officials noted that the projected increases fall far below the administration's current defense authorization request for fiscal 1986, which calls for a 6 percent increase after inflation.

Some of the increases in the latest projections are due to cost overruns on weapons.

The Pentagon reported a 22.2 percent increase in the cost of the Advanced Medium Range Air-to-Air Missile (AMRAAM), which some members of Congress have criticized for uncontrolled costs and ill-defined purpose.

The report attributes its projected cost increase, from $7.7 billion to $9.4 billion, to a restructuring of the program but says Air Force experts are looking for ways to hold down the increase.

Of the total projected cost increase, $35.5 billion results from administration plans to increase the number of weapons beyond earlier blueprints for the 1990s. Those plans have not been approved by Congress.

The extra spending would build 284 aircraft, 364 tanks and tracked vehicles, 19 ships and five satellites, according to the report.

Officials said the projected jump in the cost of acquiring more weapons would be offset by lower inflation rates and reductions in the cost and scope of other programs. As a result, the final projected increase for all 84 weapons systems would be $25.1 billion.

Programs whose costs are expected to decline include the Joint Tactical Missile System, by 39 percent; Blackhawk Helicopter, 9.4 percent; CG47 Aegis Cruiser, 3.8 percent, and High Speed Anti-Radiation Missile, 20.8 percent.

Big increases are projected for the Defense Satellite Communications System, at 35.6 percent; F16 jet fighters, 14 percent; the A6E attack aircraft, 108 percent; the Phoenix air-to-air missile, 82.2 percent, and the Apache attack helicopter, 23.7 percent.

A projected slowdown in inflation, now estimated at 4.4 percent in the 1990s, helps account for the contained cost increases despite plans for additional weapons.

Officials said the projections reflect the Pentagon's improved management techniques. "We've made a concerted effort since 1981 to control cost growth," said one official. "This shows the department's efforts have been considerably successful."