President Reagan's Blue Ribbon Commission on Defense Management yesterday recommended a major overhaul of the Pentagon's weapons acquisition system, citing structural problems "far costlier" than the well-publicized stories of overpriced coffee brewers and toilet seat covers.

Commission Chairman David Packard said the package of reforms submitted to Reagan at a White House ceremony could slash tens of billions of dollars from the annual defense budget.

Reagan pledged to quickly adopt the panel's recommendations "even if they run counter to the will of the entrenched bureaucracies and special interests." Aides have said the president hopes the report will defuse public concerns about Pentagon waste and inefficiency that have eroded support for the defense buildup.

The report comes as Reagan and Congress are tangled in a legislative battle over the president's $320 billion defense budget for fiscal 1987, which is jeopardized by the Gramm-Rudman-Hollings deficit-reduction law. A senior White House official acknowledged yesterday that the defense budget is in "deep trouble," despite Reagan's nationally televised plea for support earlier this week.

The 15-member commission concluded that there is "legitimate cause for dissatisfaction" with a procurement system marred by "overwhelmingly complex" rules, fragmented leadership, "chronic instability" in weapons programs, duplication of projects and lack of innovation.

"With notable exceptions," the study said, "weapons systems take too long and cost too much to produce. Too often, they do not perform as promised or expected."

Among structural changes urged by the panel are:

*Centralization of now-diffuse procurement authority in the hands of a Defense Acquisition Executive, who would have the rank of undersecretary of defense. He would supervise weapons research, development and acquisition, as well as overseeing defense contractors. Similar posts for each service would be filled by a civilian.

*Expansion of multiyear procurement instead of annual budgeting, and establishment of firm -- or "baseline" -- agreements for weapons requirements, production schedule and costs. Both reforms are intended to increase the stability of programs.

*Long-range defense budget planning, which would include five-year spending levels set by the president and the drafting of a military strategy by the chairman of the Joint Chiefs of Staff to achieve aims within the budgetary limits.

*Congressional approval of defense budgets every two years instead of annually, with a focus on strategy and operational theories rather than line-by-line auditing of weapons programs.

*Creation of a new post of JCS vice chairman to help the chairman with the often conflicting demands of service chiefs and to reflect the views of regional commanders.

"The nation's defense programs lose far more to inefficient procedures than to fraud and dishonesty," the report said. "The truly costly problems are those of overcomplicated organization and rigid procedure, not avarice or connivance."

Reagan appointed the panel last June amid a series of procurement scandals. Packard, who was deputy defense secretary in the Nixon administration, said at a news conference that the commission examined these "horror stories" and concluded that they only drained tens of millions of dollars, a relatively small waste compared with the costs of systemic problems.

Defense Secretary Caspar W. Weinberger, according to his spokesman at the Pentagon, has "no quarrel" with the report. "It suggests many things we would like to do."