The commander of the largest U.S. military base overseas has been suddenly transferred, apparently for annoying Filipinos at a time when American diplomats are negotiating increased Philippine control of the base.

Air Force Col. Paul Mathis, commander of Clark Air Base north of here, was transferred to March Air Force Base in Southern California after he temporarily cut off water supplies to one small community on the edge of the base and tried to close a gate in the base perimeter fence that townspeople use as a shortcut between their homes and jobs.

The incidents were thought by U.S. officials to be particularly damaging because Washington is engaged in delicate negotiations with Manila over a formula for continued U.S. use of the base. American diplomats want to satisfy Manila's demand for control of the vast, 140,000-acre facility while retaining unrestricted access to its airfield for U.S. military aircraft.

[A Pentagon spokesman said in Washington that Mathis' transfer was an "internal management decision determined by the commander of the 13th Air Force to be in the best interests of the command." He said Mathis' position at March Air Force Base is "not determined."]

The sudden transfer of Mathis has sparked reports here that he fell victim to political pressure from black market operators who have been hurt by a vigorous U.S. campaign to crack down on the illegal flow of PX goods to Philippine merchants. U.S. officials have denied Mathis' tranfer has anything to do with the PX crackdown, which they say is continuing.

Stores in Angeles City, next to the airbase, seem to have increased their stocks of PX goods recently, however, and a Philippine customs officer there says monitoring of the flow of goods at Clark has relaxed.

Military sources said the leading Air Force officer in the Philippines, of being detained and searched for stolen PX goods.

13th Air Force Commander Maj. Gen. Freddie Poston, relieved Mathis because he was brusque in his relations with Filipinos in the surrounding community. A base spokesman said Mathis' replacement, Col. John Parish, would henceforth be identified in press release by an alternate title, commander of the 3rd Combat Support Group, so that the base commander title could be easily assumed by a Filipino when one is appointed to the job at the conclusion of the U.S. Philippine base negotiations.

About 9,500 American military personnel, plus their dependents, now live at Clark. While the United States now gives military assistance to the Philippines in the range of $37 million a year, U.S. officials do not consider this as direct payment for use of Clark and Subic Navay Base. Direct payment is a principle the government of Philippine President Fredinand Marcos would like to establish at a level of about $200 million a year plus sophisticated weaponry including missiles.

Washington appears to want continued access to the bases, although some strategists question the need for them when U.S. forces can use bases in Japan and the Marianas Islands.

Mathis could not be reached for comment. He left the country on Sept. 5. A Clark base spokesman said he could not confirm reports that Mathis had canceled PX privileges for 1,764 persons and court-martialed 155 servicemen in the last nine months for PX violations. He said commissary sales had declined recently, but not by as much as the 75 percent rate that had been reported.

Some military officials suggested that Marthis' identification with a new PX crackdown arose not from any initiative on his part, but from a Marcos decree last fall that supported the crackdown and at least temporarily strengthened the U.S. effort. Philippine newspapers have generally viewed the Mathis transfer as a sign that the crackdown has relaxed.

"The dealers know they will again have their regular suplies straight out of the PX stores in the bases and from the Clark Air Base landing station," said Teodoro Valencia, the nation's most prominent columnist. "What is the Philippine government going to do about a business that is backed up by the government officials and supported by the public?"

Mathis finished only 11 months of what would usually be at least a three-year tour at Clark. Military sources said he had a good record, and had been praised for stopping PX abuses during earlier service at Kunsan Air Base in South Korea.

Rafael Lazatin, 72, mayor of Angeles City, said he had experienced no trouble with Mathis. He said the base commander had immediately restored water service to the affected Philippine community and unlocked the perimeter gate when he received complaints from Philippine officials.

Clark has been the scene of several controversial incidents between Filipinos and Americans in the last several years. On occasion, Philippine employes on the base have complained