Defense Secretary Caspar W. Weinberger has backed away from his initial resistance and endorsed major provisions of a bill to strengthen the Joint Chiefs of Staff system, Sen. Barry Goldwater (R-Ariz.) revealed yesterday.

Goldwater released a letter from Weinberger in which the defense chief laid out his revised position.

Weinberger's endorsement of the major provisions in the legislation followed a strong House vote in favor of changes and a move in the Senate to revise the JCS system.

Goldwater, chairman of the Senate Armed Services Committee but absent from a hearing because his wife has undergone surgery this week, welcomed Weinberger's move as a step in narrowing differences over Defense Department reforms but termed it "only a start."

While rejecting a committee staff suggestion to replace the Joint Chiefs system with a purely advisory group, Weinberger said he favored designating the chairman of the JCS, not the chiefs as a group, as principal military adviser to the president and secretary of defense.

He also backed placing the JCS staff under the direction of the chairman, which would give the chairman more clout. He also supported establishing a four-star vice chairman who did not outrank the service chiefs.

Three weeks earlier, reacting to the Senate committee staff report, Weinberger argued against making changes at least until a presidential panel examining Pentagon restructuring finishes its work next summer.

On another matter, Weinberger also told Congress yesterday that planned cuts in the increasingly expensive military retirement system would harm future readiness as well as the morale of the current force.

Moreover, a Pentagon study of options for reaching a new congressional target for retirement pay shows the benefits promised future enlistees will have to be slashed 16 percent, Weinberger said in a one-page letter.

Citing the recently completed Pentagon study, he said benefit cuts would prompt a "significant" loss of experienced, mid-level personnel and impose higher recruiting and training costs.

Weinberger's letter, dated Nov. 15, was attached to a 34-page report outlining two options for achieving a $2.9 billion reduction in "retirement accrual funding" ordered this fall by Congress. They were released yesterday as a Senate subcommittee opened hearings to study the two approaches.

Weinberger concluded his letter with a plea to reconsider the cutback, but there has been no evidence Congress is willing to do so. Lawmakers reduced the Pentagon's fiscal 1986 request for $18.2 billion in retirement money to $15.3 billion.

Congressional critics, led by Rep. Les Aspin (D-Wis.), chairman of the House Armed Services Committee, say the system would cost $45 billion by the end of the century unless changes are made. They also maintain that the system should reflect a modern world in which relatively few U.S. military people are likely to see combat.

The Pentagon report did not express a preference for either option. It concluded that both would result in a 16 percent reduction in military retired pay, although one would accomplish the cut by modifying the benefit formula while the other would reduce annual cost-of-living adjustments.

Under the current system, military personnel are allowed to retire after 20 years' service with 50 percent of their basic pay.