FijiFirst has garnered 42 per cent of the vote with half of all polling stations counted as of midday Saturday.
The opposition People's Alliance led by former prime minister and coup leader Sitiveni Rabuka now sits on 36 per cent.
The National Federation Party has eight per cent of the vote while the Social Democratic Liberal Party has 5.5.
The other five political parties remain below the five per cent threshold of votes required to qualify for a seat in the expanded 55-member parliament.
Bainimarama - who came to power after instigating a coup in 2006 - has a personal vote of 28 per cent in Fiji's single constituency while Rabuka is sitting at 15 per cent.
Rabuka said he remains hopeful he will be able to form a coalition government.
A final tally is due on Sunday.
The fallout from Rabuka being taken into custody and questioned by police on Friday night after writing to the military commander asking for an intervention in the election has continued.
He said he was not arrested or charged.
The party's general secretary was also taken in for questioning.
Rabuka told reporters on Friday police questioned him about his statements on the election, particularly in relation to social media posts.
"It's an occupational hazard for a political opposition in Fiji," he said when asked if he thought the developments constituted political interference.
Rabuka had wanted the military to use its powers under the constitution to oversee a fair ballot count after alleging voting irregularities.
He said it would not be a coup because the army would not be running the government.
Major General Jone Kalouniwai declined to get involved, saying using the military in the electoral process would be unconstitutional and he maintained faith in the system.
Methodist Church Reverend Ili Vunisuwai was also taken in for questioning by police after he wrote to the president and army commander and expressed concerns about the integrity of the election.
Opposition parties also doubled down on claims of voting irregularities and former prime minister and Labour Party leader Mahendra Chaudhry alleged possible fraud.
Chaudhry said he had people willing to sign statutory declarations saying they voted for him at a particular booth he recorded no ballots at when counted.
"I am personally confident hundreds of my votes have been hijacked or disappeared," he said.
"That's why I am alleging possible fraud."
National Federation Party leader Biman Prasad said his scrutineers were told to leave the ballot counting arena last night by police despite FijiFirst members still being there.
He said the number of observers had been reduced and called for their reinstatement as well as access to more tabulated raw data to verify the results.
Opposition parties are still hanging their concerns over a glitch that caused the election results app to be taken offline on election night.
People's Alliance had been ahead of FijiFirst but this swapped when the app came back online after a number of hours on election night.
The supervisor of elections, Mohammed Saneem, said votes had been mismatched to candidates when they were uploaded to the results app, causing some candidates to show unusually high numbers.
Saneem said while the app was down, a substantial number of polling stations reported their results which is what updated the overall tally.
He said there was no problem with the database as ballots are manually counted and verified.
The Multinational Observer Group says it has not observed "any significant irregularities or issues during pre-polling, postal voting or election day voting".
Co-chair and Australian MP Rebekha Sharkie expressed confidence in the ballot counting process and said extra safeguards were put in place after the glitch.
The organisation's interim report noted the app is not used to count votes, only to publish results.
This article was made possible through the Melbourne Press Club's Michael Gordon Journalism Fellowship Program.
14°C