As President Reagan's ambitious long-range defense strategy comes into clearer focus, it prompts a fundamental question. Are the traditional ways of conducting military business adequate in these days of quarter-trillion dollar defense budgets?
Concerns are being raised in several key areas: lines of authority between the Pentagon's top civilians and the military, working relations between individual services, and a federal budget process that often works against the setting and meeting of long-term goals. Some examples:
* In a recent report, the General Accounting Office (GAO) cites the need for increased efficiency in the development and procurement of weapons. And it says the Pentagon ''lacks a well-planned strategy and priority system'' for spending its increased operations and maintenance funds. The GAO warns that current pay policies will not correct the lack of highly skilled personnel and ''will yield extremely high costs by the 1990s.''
* A serious and lively debate has risen over the structure and operation of the Joint Chiefs of Staff (JCS), a debate sharpened by administration plans to build a more muscular and aggressive military. A growing number of senior officers, civilian officials at the Pentagon, and private and government military experts criticize the current system under which the services are supposed to find a consensus on military strategy.
Too often, many agree, the consensus is a bland mix designed to be as inoffensive as possible and allow the individual services to press forward with their own parochial interests. The result, critics say, can be bad advice for the Pentagon's civilian overseers and inefficient use of military resources. JCS Chairman Gen. David Jones argues that the post, from which he soon will retire, should be strengthened to give his successor authority over the other chiefs in interservice issues.
* Former JCS chairman Maxwell Taylor says that under the current congressional budget procedure, ''there is no way for Congress to know whether the budget is adequate, excessive, or insufficient to meet the needs of task readiness, although this . . . is the true measure of military adequacy.''
In recent congressional testimony, General Taylor outlined the global tasks theoretically assigned to US armed forces and said, ''The requirement in men, money, and material would likely far exceed the estimated cost of the Reagan five-year program.''
* Questions are being asked about Defense Secretary Caspar W. Weinberger's plan to decentralize certain key military management functions from the Pentagon itself to the individual services. Unless carefully controlled, says Herschel Kanter of the Institute for Defense Analyses, this could work against an integrated military strategy in which the services increasingly will have to support one another.
These observations and warnings are significant because in many cases they come not from traditional Pentagon critics, but from strong defense advocates, including high-ranking military officers.
''We need to spend more time on our war-fighting capabilities and less on an intramural scramble for resources,'' says General Jones. Senior defense specialist John Collins of the Congressional Research Service also criticizes this ''dual hat'' system in which members of the JCS head their own service branch. The JCS, says Collins (a 30-year Army veteran), ''can always agree on more for everybody. And since this is the path of least resistance, it is often taken.''
Recent Pentagon directives and statements by senior administration officials have been interpreted as a scaling back of military ambitions and more realistic attitude toward setting priorities. But as yet, there has been very little administration give on its record defense budget. Under Mr. Weinberger's ''controlled decentralization'' program, writes Dr. Kanter in the current issue of Strategic Review, ''the services can be expected to emphasize their own priorities.'' Balancing needs for an orderly budget and long-range program, he says, requires a high level of White House-Congress cooperation that ''is more essential than ever.''