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The ruling Fiji First party led provisional national election results, boosted by a 31.42% vote for Prime Minister Frank Bainimarama, with half of polling stations counted in the Pacific island nation on Thursday.

Bainimarama, who came to power in a coup 16 years ago, is contesting his third democratic election since reforms to Fiji's constitution in 2013 scrapped a system that drew distinctions between the votes of indigenous Fijians and its large ethnic Indian population.

He is in a tight race against another former coup leader and one-time prime minister, Sitiveni Rabuka, whose People's Alliance Party has formed a coalition with Fiji's oldest political party, the National Federation Party.

The provisional result from Wednesday's vote showed Fiji First with 45.88% of votes at 7 a.m. Thursday, ahead of the People's Alliance Party with 32.66% of votes, while the National Federation Party had 9.29% of votes.

With 1,238 out of 2,017 polling stations counted, Bainimarama had personally garnered 31.42% of all votes in Fiji's proportional representation system, where there is a single constituency, and Rabuka had 16.34% of votes.

The final result, based on a manual count of voting papers, will be known on Sunday, election officials said.

Technical problems which plagued the election office's app, used by the public to track provisional results called in from election booths on Wednesday evening, has fuelled mistrust among opposition parties.

The app had shown a People's Alliance Party candidate leading, before it was taken offline around 11 p.m. on Wednesday and the election office told media there were errors. When the app came back at 2.30 a.m., it showed Fiji First ahead.

The election office said mistakes had been made transferring data to the app, which had incorrectly boosted some candidates vote.

Rabuka told reporters at a press conference on Thursday his party was "not satisfied", and is writing to the Supervisor of Elections, the army commander and Fiji's president.

Leaders of five opposition parties issued a joint statement on Thursday afternoon, calling for a halt to counting, saying the "glitch" had caused serious problems and they demanded an independent audit of the electoral system.

Fiji's election commissioner, Mohammed Saneem, responded by telling media a "double blind data entry" system was being used to avoid errors in the final count, which was fully manual, and each party was entitled to have agents present.

Voter turnout was less than 60%, which analysts said was the lowest in a decade.

A multinational observer group led by Australia, India and Indonesia includes 90 election observers.

Australian Foreign Minister Penny Wong told reporters Fiji's election appeared to have been conducted "peacefully and in an orderly manner". (Reuters)