Some voters were kept waiting for four hours in the capital, Suva, and the rural west of the main island of Viti Levu.
The delays added to a tense build-up to the week-long election, and police and the military said they would not tolerate incitements to racial hatred. Fiji has suffered three racially motivated coups and a bloody army mutiny since 1987.
The poll pits Laisenia Qarase, the indigenous prime minister, against Mahendra Chaudhry, an ethnic Indian who was ousted from the post in 2000 by armed nationalists. Both candidates predict that they will win a majority in the 71-seat parliament.
Indigenous Fijians, who make up 51% of the 906,000 population, fear that the economic clout of ethnic Indians, who dominate the sugar- and tourism-based economy, will be matched by political power.
"It's a pain. I've got my granddaughters here and they haven't had their breakfast"
Would-be Fijian voter
Residents in the racially mixed village of Sabeto were angered by the voting delays. One, Sohrab Ali, was told to leave and return later.
"It's a pain. I've got my granddaughters here and they haven't had their breakfast," he said. "I was here on time. We're trying to be responsible and vote."
Chaudhry, leader of the Fiji Labour party, pinned the blame on the election supervisor, Semesa Karavaki, and called for his resignation. Karavaki was absent because of religious beliefs.
"Look at the mess he's made and he's not at work today," Chaudhry said.
Karavaki's deputy apologised, blaming the delays on logistical problems. "We assure you that it will be 100% ready on Monday," Semi Matalau told a media conference.
Voting will stop on Sunday and resume on Monday for another six days.
International observers were concerned by the long delays.
Istvan Szent-Ivanyi, leading a team of EU observers, said: "It showed me that the election has not been prepared in a proper way."
Police were present at voting stations but there were no security incidents reported.
Frank Bainimarama, head of the Fijian military, has clashed with Qarase several times in the past year and urged his troops not to vote for Qarase's Soqosoqo Duavata ni Lewenivanua party.
He also warned candidates against inciting racial hatred after Qarase said Fiji was not yet ready for an Indian leader. Qarase and Bainimarama cast their ballots in the same Suva polling station but did not speak to each other.
A result is expected to be known on May 18.