The Defense Department's assistant secretary for health affairs, Dr. William E. Mayer, has proposed halting the sale of cigarettes in military commissaries and raising the price of those sold in military exchanges to reduce what he considers excessive smoking, according to Pentagon sources.

A directive containing Mayer's proposals, along with an alternative that recommends doing nothing about cigarette sales, is awaiting a decision by Defense Secretary Caspar W. Weinberger, according to sources in the Pentagon and on Capitol Hill.

"There has been a delay," one source said, because tobacco revenue is a politically sensitive issue.

In 1982, the most recent year for which Pentagon statistics are available, 127 million cartons of cigarettes costing $572 million were sold in military commissaries, post exchanges and clubs.

In 1983, cigarettes made up 10 percent of all commissary sales, at prices discounted 35 percent below those in civilian stores. At post exchanges, cigarettes typically sell for 20 percent less. According to other Pentagon data, 52.2 percent of service personnel under the age of 20 smoke, compared to 21.2 percent of high school seniors.

One reason for the delay of the health directive was a congressional move last month, led by Sen. David L. Boren (D-Okla.), to reduce smoking by increasing the price of cigarettes sold on military reservations. Approved by the Senate, the proposal was blocked in a House-Senate conference by a House Democrat from the tobacco-growing state of North Carolina, Rep. W.G. (Bill) Hefner, according to House sources.

The Boren price-increase proposal had been added to the defense spending bill by Sen. Ted Stevens (R-Alaska), chairman of the Senate Appropriations defense subcommittee and a strong opponent of smoking. Stevens has introduced a measure of his own to bar smoking in federal buildings.

Stevens also called for a $77 million reduction in the $600 million federal fund to subsidize commissary operations, on grounds that the subsidy for cigarette sales was no longer needed. The commissary, the military version of a supermarket, is considered an important benefit by both active and retired service personnel because by law its prices are discounted.

Opposition to the Boren amendment came from a broad group of organizations, including many worried about the precedent for cutting back on commissary privileges.

The Non-Commissioned Officers Association and the Veterans of Foreign Wars were among those lobbying against it, according to a spokesman for the Tobacco Institute, an industry lobbying group.They were drawn less by the smoking and health issue, the spokesman said, than by a "whittling away of commissary rights."

A Hefner aide said the congressman helped eliminate the Boren amendment while persuading the conferees to request a report from Mayer, to be delivered by March 1, that would "determine the effects of cigarette prices on military consumption patterns, the health of military personnel and the economic cost to the military and society."

The aide said a congressional effort to raise cigarette prices for the armed forces "had never come up before" and he was "not certain what would happen next."

At the Pentagon, an official following the Mayer proposals said he expected Weinberger to "address the question in the not distant future."

The official said Mayer has several times testified before Congress of his concern that low cigarette prices encourage smoking by military personnel.

"What is going on," the Tobacco Institute spokesman said, "is a Pentagon staff dispute, with the health affairs people and other antismoking forces on one side and a number of other people looking at the broader issue of commissary rights."