Hondurans voted for a new president and legislature today in national elections. Many voters were delayed by confusion over U.S.-supplied indelible ink, initially invisible, designed to prevent fraud.

Despite the initial delays, Hondurans appeared to turn out in large numbers for the election that is to provide the first democratic transition from one civilian president to another in half a century here.

Jose Azcona of the ruling Liberal Party and Rafael Leonardo Callejas of the opposition National Party moved into a close race, according to the first unofficial returns that began coming in late tonight. The two were considered the principal contenders to replace President Roberto Suazo Cordova for a four-year term.

Barring collapse of the electoral process after the vote, diplomatic and Honduran political officials said, the outcome was unlikely to affect key Central American policies of the Reagan administration. Both leading candidates have indicated an intention to pursue Suazo's cooperation with the Honduran armed forces in organizing U.S. military maneuvers here and allowing U.S.-sponsored anti-Sandinista rebels to use the country as a haven and logistical base.

The ink, into which voters' fingers were dipped to prevent multiple voting, was part of $600,000 in materials provided by the United States, said an embassy spokesman. Another $300,000 brought in about 300 foreign observers, including a 13-member U.S. delegation.

One observer invited by the Honduran government was Arturo Cruz of the United Nicaraguan Opposition, an umbrella group of the anti-Sandinista guerrillas fighting to overthrow the government of neighboring Nicaragua.

The colorless ink was manufactured in the United States as a 20 percent solution of silver nitrate to guarantee that a stain -- which depended on the skin's reaction in natural light -- would remain visible on a voter throughout the day, the spokesman said. But the coloring took so long to become apparent in the weak light of dawn that many precinct captains became convinced that it was not working and refused to allow voting to begin.

"Look. It's pure water," shouted one woman helping at a suburban voting table. She held up a piece of paper dipped into the ink with no visible result.

Hondurans, given a history of voting fraud, are suspicious of voting mechanisms. Partly as a result, voters and precinct captains were unwilling to allow voting to begin until it became apparent that the ink would produce an indelible mark.

This took an hour in many precincts and longer in others, delaying the start of voting that had been scheduled for 6 a.m. Because of the confusion, the National Election Tribunal decided at midafternoon to prolong the voting schedule one hour to a 6 p.m. close.

The U.S. Embassy spokesman, Michael O'Brien, said written instructions had gone out to polling places explaining how the ink worked. But visits and reports from around the country indicated that many voting officials and voters were unaware of the stain's sluggishness until they experienced it. About half the country is illiterate, according to a State Department estimate.

Scores of cars and trucks flying the Liberal and National party flags sped through the narrow streets of Tegucigalpa calling followers out to polling places.

A number of voters, including party activists, said they still did not know how the ballots would be tallied to decide on the winner. The election serves as both a primary and a final election, with parties fielding more than one presidential candidate -- an unusual but not unprecedented system in Latin America.

The National Election Tribunal -- succumbing to pressure from candidates, the armed forces, the U.S. Embassy and the Roman Catholic Church -- decided only late last night to follow the terms of an electoral law as modified last June.

The law provides that the presidency goes to the top vote getter within the party that gets the most overall votes. But the National Party leadership has contested its legality, pointing out that the constitution says the presidency goes to the candidate with a simple majority, without reference to his party's vote. The National Party delegate on the tribunal reaffirmed that stand last night, refusing to join the other four tribunal members in voting to abide by the electoral law.

Callejas has pledged to abide by the tribunal decision. But the refusal by his party leadership has kept open the possibility of a Supreme Court challenge and political maneuvering after the election.