President Reagan has signed an executive order that makes the Pentagon the final arbiter in most contract disputes between the military and labor unions that represent U.S. civilian employes at overseas military bases.

The order, seen as a major setback for the unions, will prevent them from appealing certain disputes to the Federal Labor Relations Authority. Instead, they must live with the Pentagon's position on any bargaining issue that DOD decides could disrupt relations between the United States and the country where the base is located.

Reagan's decision is a "direct attack on the entire labor movement," said Catherine Waelder, an attorney for the National Federation of Federal Employes. She accused Reagan of "deliberately sabotaging" the rights of overseas civil servants to fair labor negotiations.

Reagan issued the order last week, after the Pentagon convinced him that union bargaining overseas could "exacerbate relations with host governments," the White House said. The president said the danger was so great that "the suspension of certain labor-management relations provisions is necessary in the interest of national security."

While the order applies to all overseas DOD civilian employes, except those in Panama, it is aimed at ending a dispute between Local 1363 of the NFFE and military officers in the Republic of Korea, the White House said.

Nearly three years ago, the 300-member local demanded that Gen. John A. Wickham, then commander of U.S. forces in Korea, negotiate what products would be rationed at military post-exchanges (PXs) and the number of vehicles that employes could bring duty-free into Korea.

Wickham refused to bargain, claiming those items were restricted as part of Status of Forces Agreements (SOFA) between South Korea and the United States. The restrictions were necessary to limit black-market trading in Korea, Wickham said. Allowing the unions to negotiate about such items, would be the same as allowing a union to negotiate a diplomatic agreement with Korea.

The union appealed Wickham's decision to the FLRA, which ruled in its favor in 1980. Arbitrators said PX goods and duty-free vehicles were "conditions of employment" -- job benefits offered by the military to attract employes and, therefore, negotiable under the Federal Service Labor-Management Relations statutes. DOD immediately asked Reagan to suspend portions of those statutes and appealed the FLRA decision to the U.S. Court of Appeals for the Federal Circuit. In August, that court ruled in favor of the union and ordered the new commander in Korea to begin negotiations.