There is more than coincidence behind Secretary of State Edmund S. Muskie's repeated slips of the tongue identifying himself as "secretary of defense." Muskie has the Pentagon on his mind these days, and he is far from happy about its role in this country's international affairs.

Muskie and senior associates of his, in talks with reporters after Los Angeles and San Francisco speeches last week in which he mistakenly called himself head of the military arm of government, said there is no personal conflict with Secretary of Defense Harold Brown.

Nevertheless, Muskie made clear his view that failures of coordination between Pentagon and State Department are more serious for foreign policy than the widely heralded conflict between the secretary of state and the presidential national security affairs adviser, Zbigniew Brzezinski.

The cause of Muskie's most recent unhappiness was a newly signed presidential directive ordering a sweeping revision of U.S. strategy in a nuclear war against the Soviet Union. Muskie had heard limited discussion of this in one of his regular luncheon meetings with Brown and Brzezinski, but had no idea that a policy change was close to fruition until he read The Washington Post and The New York Times last Wednesday morning.

Questioned about the new strategic doctrine on the way to his California speaking engagements late Wednesday, Muskie expressed his displeasure. He spoke to Brown about the matter by telephone from Los Angeles, and later received a call from the defense secretary offering a detailed briefing in the coming week.

Department officials said State was involved in the nuclear war study many months ago, before Muskie replaced Cyrus R. Vance as secretary. Muskie said he does not believe he was deliberately excluded from the final phase of the study, but he made clear he would like to have been consulted.

Concerns about both procedure and substance appear to figure in Muskie's unhappiness.

On the procedural side, he expressed frustration at a lack of sufficient time for thorough examination of all the consequences of foreign policy decisions. In his first three months, some of the formal decision-making apparatus has struck Muskie as superficial, often more of a facade of serious study than the real thing.

In advance of the Pentagon briefings, Muskie has been reluctant to venture an opinion about the substance of the change in nuclear weapons targeting. But when a similar change was proposed in 1974 by then Secretary of Defense James R. Schlesinger, Muskie the senator thought it was a poor idea that could increase the danger to an already imperiled world.

In a Voice of American interview yesterday, Brzezinski said the new targeting strategy, which shifts targeting of U.S. nuclear weapons from population centers to political and military command centers in the Soviet Union, was undertaken to avoid "an apocalyptic choice" between a "massive instant war" or capitulation.

Brzezinski said the president's directive is "designed . . . to permit bargaining even in the context of a crisis."

The assignment of targets for U.S. strategic nuclear weapons is a matter of far-reaching importance to relations with the Soviet Union. It also affects the military and political strategy of individual allies and of alliances. What might seem at first glance a purely military question, therefore, is laden with political and diplomatic significance.

According to Muskie's associates, he also is concerned about several other aspects of military-related activity:

The "rapid deployment force," which he originally understood to be a means of accelerating limited military responses to challenges in remote areas, may be evolving into a larger and more strategically significant outfit. Muskie is said to question whether the requirement for and consequences of this have been fully explored.

The far-ranging travels and proposed travels of Pentagon officials are disturbing to Muskie because of his apprehension that decisions are being signaled or struck without full consideration. Among the travels that have raised questions in the Foggy Bottom executive suite is a proposed globe-girdling trip by Undersecretary of Defense Robert Komer, who is renowned for bureaucratic boldness.