After three years as the strong man of El Salvador's U.S.-backed Army, Defense Minister Jose Guillermo Garcia is expected to leave his post within three months, according to senior military and civilian officals here.

Private confirmation of Gen. Garcia's expected departure follows a six-day mutiny against his leadership that ended Wednesday. The officers' rebellion in Cabanas province is seen as a symptom of what these officials say has been a growing disenchantment with the man who has held the powerful Defense Ministry since 1979 through three otherwise complete changes of government.

For both the Reagan administration and the civilian and military leaders it supports here, Garcia's likely resignation could be a mixed blessing. He increasingly is seen as an impediment to effective military strategy against leftist guerrillas.

The officials indicate that his departure could help bring about tactical military changes that Washington seeks--and also shifts in the leadership of those security forces often associated with the country's human rights problems--if several of the defense minister's longtime associates are also removed.

But some officials are concerned that the U.S.-endorsed agrarian reform here will lose a vital patron if Garcia goes and that the ultra-right will be able to take general advantage of a resulting confusion in the Army.

Garcia has made no public indication of his intention to resign and there is strong sentiment among many officers that he should not do so in the wake of a mutiny. But as one influential commander put it, "Things have been piling up for Gen. Garcia. One thing after another. And he will fall finally, as if pulled down by gravity. It's impossible for someone to hold onto a position when he has so many problems."

Another high-level officer close to the defense minister said, "Garcia is a conscientious man who's not going to wait till some night President Alvaro Magana calls him on the telephone and tells him he has to resign. He will go peacefully."

Garcia is reported to have an eye disease that may need surgery, and there are some rumors that this will be used partly as a pretext for his resignation.

A well-informed government official familiar with the inner workings of the armed forces described several groups in the Army who want to see Garcia out. Among them they appear to form a majority. One group is essentially made up of left-leaning young officers associated with the liberal "military youth" movement that seized power in a 1979 coup and was crushed by Garcia in 1980.

Another small group consists of soldiers punished by Garcia for infractions of the military rules but who are still on active duty.

A third group, motivated by personal ambition or by ideology or by both, is tied to right-wing interests, including Constituent Assembly President Roberto D'Aubuisson's party. This group would roll back the agrarian and other reform programs aimed at dispersing the wealth of the oligarchy that has run the country.

After years of equivocation on the reforms, with politicians left to carry out what many in the armed forces were believed to oppose, Garcia came down solidly in favor of the changes last June. This stopped right-wing attempts to cancel the changes.

Shortly after that, prominent members of private business organizations began publicly questioning the defense minister's conduct of the war. It is because of Garcia's stand on reforms that he has been "condemned by the right," said one of his associates.

The more widespread complaint among officers against Garcia is of cronyism and maintenance of personal power at the expense of the war effort.

"This is the group of officers," said one senior commander, "who have seen logistical failings in the high command; the captain who goes three days without food for his troops in Morazan waiting for someone to get around to sending it.

"This Garcia is concerned with other things. The stories that he was thinking of running for president did not sit well with these people."

According to this official and to well-informed military observers, Garcia has left controversial commanders, such as Col. Francisco Moran of the notorious Treasury police and Col. Napoleon Alvarado of San Vincente province, in positions of power because they are close friends and could be counted on to support him in the Army's internal struggles.

Alvarado and other troop commanders with close ties to Garcia in embattled rural El Salvador have been reluctant in many cases to adopt the kind of small-unit, aggressive patrols that U.S. advisers advocate. This apparently has played a role in the U.S. Embassy's public position of maintaining strict neutrality with regard to the current pressures on Garcia. In the past, especially during the past year, the embassy had been his staunch ally.

One of the defense minister's fellow officers, commenting on the changing currents in the Army, credited Garcia with "saving the armed forces from what was considered by many soldiers leftist-inspired dissension in their ranks two years ago.

"Now, even at social functions few people make an effort to ingratiate or even associate themselves with the minister. People don't want to be in good with him the way they once did."