With over 325,000 of the 500,000 votes counted from more than 1100 polling stations just before 5am, Mr Bainimarama has a commanding lead.
Mr Bainimarama first seized power to become prime minister in a 2006 military coup.
Yesterday's election was Fiji's first in eight years and the first since the coup.
Mr Bainimarama has 142,000 votes and his Fiji First Party is in a decisive lead with more than 200,000, or nearly 62 per cent, of the votes.
Seven political parties and 248 candidates, including two independents, contested in the polls.
Polling closed at 6pm, but counting was still continuing 11 hours later.
Supervisor of elections Mohammed Saneem said voter turnout was high, with most centres reporting between 77 and 100 per cent voting.
About 520,000 people cast their votes at 1460 polling stations across Fiji, according to the Fijian Elections Office.
The Multinational Observer Group, which has been observing the elections, will be releasing their preliminary report this afternoon.
