Militant Filipino strikers continued to block Subic Bay Naval Base this morning, after U.S. and Philippine negotiators had agreed to end a bitter strike and blockade against all U.S. military facilities here.

While strikers reportedly took down barricades at most of the U.S. bases, left-wing union members rejected a compromise reached Tuesday evening and continued to prevent most Filipino base employes from returning to work at Subic. At Clark Air Base and six smaller facilities, the tentative agreement appeared to have ended the 11-day strike, which has taken on anti-American overtones.

The labor dispute has been seen as the angriest in the history of the strategically important and politically sensitive bases.

Representatives of the U.S. Embassy and the Philippine Labor Ministry joined the negotiations yesterday and crafted a compromise that includes an immediate end to the strike and removal of the barricades; additional benefits, such as a quarterly rice subsidy, for workers, and further talks to resolve minor issues. Deputy Labor Minister Carmelo Noriel said the employes were due to begin returning this morning.

But largely left-wing union members, gathered at the gates to Subic, shouted down their leaders in the early-morning hours today and vowed to remove them from office for having signed the compromise. Witnesses said union officials left and armed police moved into the main gate area when protesting hard-liners threatened violence.

A base spokesman, Lt. Cmdr. J.D. Van Sickle, said that Philippine police and troops had cleared only one of Subic's three main gates in time for the Wednesday morning shift. He said that strikers continued to demonstrate near the open gate and that only a few Filipinos had entered the base.

The 22,000 union members, about half of the Filipino work force on the bases, walked out on March 21, when Defense Department officials in Washington vetoed a tentative contract agreement that had awarded severance pay to the union members. The workers erected the roadblocks to help enforce the strike. U.S. military officials said the roadblocks violated the 1947 bases agreement, which guarantees free access to the facilities.

Early in the strike, 12 persons were injured in fights between strikers and military personnel who tried to get into the bases. Filipinos accused servicemen of stabbing strikers, a charge denied by base officials.

During the strike, U.S. officials had declared bars and nightclubs in towns near the bases off-limits to U.S. military personnel in a move that sharpened opposition to the strike from owners of small businesses and their employes who rely on the bases for their clientele.

U.S. officials, such as the Subic Bay commander, Rear Adm. Edwin Kohn, consistently have played down any interpretation of the strike as a Philippine-American conflict.

But among some young workers and leftists, "an anti-American feeling did add a little note of venom" to the strike, said a U.S. source who asked not to be identified.

"This is the bitterest confrontation ever" at the bases, said Mayor Richard Gordon of Olongapo City, adjacent to Subic Bay Naval Base.

A western labor analyst reflected a general view that, in the freer political atmosphere following the fall last month of president Ferdinand Marcos, the Philippine labor movement will become more demanding.

In another development, the government of President Corazon Aquino announced yesterday that it was retiring 39 senior military officers, including 20 generals, who had been kept on past retirement age by Marcos.

Under Marcos, as many as 60 generals had been permitted to remain active beyond retirement age primarily because of their personal loyalty to Marcos, his family and his friends. Their presence has caused deep morale problems within the Philippine military, and, during the presidential campaign, Aquino pledged to retire them.

In announcing the decision, presidential spokesman Rene Saguisag said Aquino temporarily had retained 11 overage officers whose services were deemed necessary.