Sitiveni Rabuka's People's Alliance party has garnered almost 55 per cent of the vote compared to 22 per cent for Prime Minister Frank Bainimarama's FijiFirst in final results from 13 per cent of voting stations.
The Social Democratic Liberal Party has eight per cent and the National Federation Party five.
The other five political parties remain below the five per cent threshold of votes needed to qualify for a seat in the expanded 55-member parliament.
Both Bainimarama - who came to power after instigating a coup in 2006 - and Rabuka have garnered 13 per cent of the vote in Fiji's single constituency.
Opposition parties had raised concerns over the preliminary count after results changed dramatically when the election's app was taken offline due to a glitch.
People's Alliance had been ahead of FijiFirst but this swapped when the app came back online after a number of hours on Wednesday, election night.
The supervisor of elections said votes had been mismatched to candidates when being uploaded to the results app and caused some candidates to show an unusually high number of votes.
It was corrected when it was taken offline, wiped and data re-uploaded.
Mohammed Saneem said there had been no problems with the official voting data as the system used for the count is offline and data is plugged in after ballots are manually counted and numbers are verified.
He said while the app was down, a substantial number of polling stations reported their results which is what updated the overall tally.
But Rabuka and the leaders of three other opposition parties said they would refuse to be sworn into parliament if elected if there was no independent oversight of a recount.
All declined to express faith in the Fijian Elections Office.
The influential Methodist Church in the deeply religious nation has also expressed its concerns over the integrity of the election.
In a letter addressed to Fiji's president, Reverend Ili Vunisuwai said he wasn't convinced by the supervisor's explanation of the discrepancy.
"While there were explanations of the glitch provided, it was not convincing to restore the confidence of our members," he wrote.
"Since this is not the first time this has happened, the Church is deeply concerned with the continuous anomalies in the FEO and wishes to advice (sic) that we had lost faith and confidence of the affairs of this institution and its systems."
The reverend called for the president's intervention and copied in the military commander, the police commissioner and the Fiji Electoral Commission chairman.
Rabuka - a former prime minister and 1987 coup leader - said he would write to the military commander and ask him to use his powers under the constitution to intervene.
Fiji's constitution gives the military the responsibility "to ensure at all times the security, defence and well-being of Fiji and Fijians".
Fiji's military commander has told his soldiers to respect the outcome of the election and said anything less would be an affront to democracy.
Asked if flagging military intervention would spark anxiety in a nation with a history riddled with coups, Rabuka said it would not be a coup.
He said the military would be acting in line with the constitution if it accepted his proposal.
"It will be supporting the civilian system that is running," he said.
"They will not come in to run the government. They will not come in to act as ministers."
At least half of the 120 votes cast at the Republic of Fiji Military Forces strategic headquarters polling station were for Bainimarama, with Rabuka polling less than 10 per cent.Â
The Multinational Observer Group says it continues to monitor the situation and is due to release its interim report on Friday evening.
This article was made possible through the Melbourne Press Club's Michael Gordon Journalism Fellowship Program.
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