After three years of wavering, Bahrain has finally decided to end the home port privileges of the U.S. Navy's Middle East force, Foreign Minister Mohammad Bin Mobarak Khalifa said yesterday.

The three-ship fleet will still be welcome to call here and take on supplies, he said, but after June 30, the former British naval base at Fufair will no longer to be home port of the fleet's flagship or the headquarters of its commander.

The fate of the American installation here - which all involved insist is a "facility" and not a base - has been the subject of negotiation for many months between the United States and Bahrain. The Persian Gulf island and San Diego Garcia, have been the only American onshore commands between the Philippines and the Mediterranean.

Khalifa indicated that a formula has been found that will allow the Americans to continue to use Bahrain - with its strategic location and modern airport - to supply and service the Middle East fleet, without leaving Bahrain open to charges of harboring a U.S. military base.

"If a ship would like to come here, yes, of course," he said. "They will have to make a request each time, but we will make arrangements. They will be welcome to take supplies. But we don't want the U.S. presence in such a way" that it could be construed as a base and give other Persian Gulf or Indian Ocean countries and excuse to allow foreign powers to put in military bases.

Rear Adm. William J. Crowe Jr., commander of the fleet, said his ouster from Bahrain and the ending of home port privileges for his flagship would mean a "fundamental change" in the American relationship with Bahrain. He said, however, that the most important part of the new arrangement is that the ships will still be allowed to take on supplies here.

"If we can still come in, I can do what I have to do," he said.

The Navy has operated out of this tiny island for some 30 years, first as tenants of the British and since Bahrain's independence in 1971 by agreement with the government of the emir Sheikh Isa Bin Sulman Khalifa.

During the 1973 Middle East war, when the United States angered the Arabs by airlifting supplies to Israel, Bahrain announced that the American were no longer welcome. There were 250 Naval families stationed here then but in anticipation of departure, the Navy has reduced that figure by attrition to about 50.

The Bahrainsis held off enforcing their ruling, however, and in 1975 granted the United States a two-year extension. That is the arrangement that the foreign minister said will not be renewed when it runs out next month. The new arrangement takes effect June 30.

In numbers, the issue hardly seems to be of much strategic importance. Crowe's fleet consists of three ships - two destroyers that are assigned here on a rotating basis from the United States, and his flagship, the U.S.S. Lasaile, a converted assault landing ship equipped with special electronic gear.

But this little fleet patrols a wide expanse of water that includes some of the world's most volatile spots - the Gulf of Suez, the Horn of Africa, the oil transport lanes of the Persian Gulf and the Indian Ocean.

Having a home port here, Crowe said, with the right to put in and resupply whenever necessary, gave the fleet a flexibility and maneuverability it would not otherwise have had. Under the new arrangement, Crowe will operate what is called a "float command," with fleet headquarters abroad the command ship and not at a home port.

He said he was encouraged by Bahrain's agreement for the Navy to keep operating the Department of Defense school here. The naval personnel who would he required to equip, maintain and supply the school could peesumably work on American ships whenever they came to port, as they do now.

It would be highly unusual for the Pentagon to operate a school in a country where there are no American military dependents, but there are signs that it may do so here because of the United States' special relationship with Saudi Arabia.

There is a large American community in Saudi Arabia around the Arabian American Oil Co. town of Dhahran, just a few miles across the water from here. The Saudis have declined to permit the Americans there to open their own high school. But it would suit the convenience of the Americans, the Bahrainis and the Saudis if the school here were kept in operation. Bahrain is to be linked to Saudi Arabia by a causeway in a few years.

Adm. Crowe said he had no other place in his territory in mind as a possible alternative home port.The former British base on the Omani Island of Masira is not suitable, he said, because it has no harbor.

He also said that after the recent of the American military mission from Ethiopia, his ships have stopped putting into that country's Red Sea ports for refueling.