Congress may deny further economic or military aid to the Philippines if last week's presidential election there is shown to be "fatally flawed," Senate Foreign Relations Committee Chairman Richard G. Lugar (R-Ind.) said yesterday.

Lugar, co-chairman of the U.S. observer mission that witnessed the election in that important Asian country, said at a news conference in South Bend, Ind., that "I would probably support curtailment of assistance" if the vote is shown to be fraudulent.

Lugar's statements came as Rep. Stephen J. Solarz (D-N.Y.), chairman of the House Foreign Affairs subcommittee on Asian and Pacific affairs, said information possessed by the Reagan administration shows that as many as 5 million Filipinos were disfranchised in order to tilt the electoral scales toward Philippine President Ferdinand Marcos.

"These figures are the smoking gun of electoral fraud," said Solarz, a leading congressional critic of Marcos. A State Department spokesman said, however, that the vote count in the Philippines, according to reports from the U.S. Embassy there, is too uncertain to draw firm conclusions.

Congressional sources said Allen Weinstein, head of the nonprofit Center for Democracy and a member of the U.S. observer mission, is to return to Manila tonight with several staff members to continue monitoring the vote count. Continuation of the work of the observer mission is expected to be announced officially today.

Special White House envoy Philip C. Habib, also expected to fly to the Philippines tonight, was given his instructions by President Reagan yesterday in a 10-minute meeting before Reagan left Washington for a political stopover en route to a California vacation until Saturday.

White House spokesman Larry Speakes said Habib's mission is "just an opportunity to assess the situation."

Another White House official, who asked not to be quoted by name, said part of Habib's goal would be "to try to bring the parties together" and to work toward a result in the Philippines that "would not undermine the process of democratization."

Habib, known for blunt language in private and lack of comment in public, was said by a senior State Department official to have "mainly a listening brief."

Lugar is reported by congressional sources to have appealed privately to Reagan in a White House meeting Tuesday not to accept a Marcos victory on the basis of present evidence.

Yesterday, he emphasized that the election process is not finished but said he is discouraged that voting returns continue to dwindle as the Philippine National Assembly begins its formal count to determine the winner.

"An economic resurgence in the Philippines is badly needed," Lugar said. "The dilemma is that, if it the U.S. aid is administered by a government which the United States does not trust, it may not be sent."

Solarz said State Department projections before last week's voting were that about 23.5 million Filipinos would cast ballots, about 90 percent of an estimated electorate of 26 million.

But reports from the National Movement for Free Elections (Namfrel) indicate that about 13 million votes have been cast in 70 percent of the precincts, which suggests that only 18 million to 19 million votes will be reported, Solarz said.

Solarz said the shortfall of 4 million to 5 million votes is the result of "a systematic and nationwide effort at disenfranchisement," especially of those likely to vote for Marcos' challenger, Corazon Aquino.

He said the U.S. Embassy estimated that 400,000 to 660,000 Philippine citizens were disfranchised in Manila alone and that information received by the embassy increasingly suggests that a major disfranchisement campaign has taken place nationwide.

Solarz predicted that uncounted votes, from areas of Marcos' greatest strength, will put the Philippines president "over the top" for reelection. However, "Once Marcos is proclaimed a winner, it will bring the country to the brink of civil war," Solarz added.

State Department sources said a major shortfall in the expected vote total seems probable but cautioned against definite conclusions until final returns are tallied.