Foreign observers here for Friday's presidential election began leaving Manila for sites in the provinces today, as Philippine officials agreed to bend the rules and let the observers inside polling stations during voting.

The Philippine Commission on Elections previously had said that the 100 or so foreign observers would have to stay more than 50 yards away from the polling places. But today, commission officials told Sen. Richard G. Lugar (R-Ind.), leader of a 20-member U.S. team appointed by President Reagan, that they would be able to go inside.

The rule had been criticized as limiting the observers' ability to do their job. The commission reaffirmed, however, that the rule would remain in effect for journalists, to "prevent confusion, overcrowding and commotion."

Lugar's group was briefed today by the U.S. Embassy and by Philippine election officials and the main citizen observer organization.

The U.S. team had breakfast with Nicanor E. Yniguez, speaker of the National Assembly, who proposed the formation of a joint legislative group to study the future status of U.S. military facilities in the Philippines, according to a government statement.

Later, some members flew to provincial towns to be in place for the start of voting Friday morning. Two other observer groups also will be in the field: a U.S. Embassy team and a 44-member international delegation organized jointly by the U.S. Republican and Democratic parties.

In a speech at a crowded lunch sponsored by the Rotary Club of Manila, the American Chamber of Commerce of the Philippines and a group called Republicans Abroad, Lugar said "our mission is not to enforce, to arbitrate, to mediate . . . but simply to observe the work of good friends."

Lugar said his team would not make judgments on the fairness of the election but would watch carefully those made by Filipinos.

He praised the Philippines for its "remarkable laws in terms of the checks and balances, the thoughtfulness which has preceded each stage." But he said the basic question is "the political will to make it work."

Lugar referred to President Ferdinand Marcos and opposition challenger Corazon Aquino as "two great leaders in this country." He called the Philippines "one of the greatest democracies that our world has produced."

Taking questions, Lugar rejected a suggestion that his people should move around unescorted. He said he had told them always to identify themselves at polling places "so that we come not as intruders, not as busybodies attempting to muddy the waters."

Lugar was asked about a full-page ad placed in a progovernment newspaper this morning by a group calling itself the Coalition of Writers and Artists for Democracy. It criticized him for questions about the fairness of the election that he voiced before he arrived.

Lugar acknowledged that he was a skeptic, but he said that "that is a person who questions, who probes, who is a genuine student of process."