Mr Bainimarama's closest rival, Sitiveni Rabuka's Sodelpa, was sitting on 38 percent of the vote at the latest tally.
The National Federation Party had 7.5 percent and was the only other party so far to have passed the five percent threshold to gain seats.
Voter turnout ranged from 53 percent to 61 percent in Fiji's four divisions, according to the Fijian Elections Office.
Pouring rain and flooding yesterday forced the closure of 26 stations on polling day affecting 7800 people.
A date has yet to be set for them to vote and a campaign blackout with accompanying media restrictions has been extended.
Final vote counting has begun after 70 percent of polling stations had phoned through their results overnight.
Official result sheets are being brought in from all over Fiji to the National Results Centre for tallying with the votes which were cast last week in Fiji's remote areas as well as those votes which were posted in.
There was confusion at the end of provisional vote counting in the 2014 election with claims of fraud and vote-rigging.
"We wish to ensure nobody makes misinformation about this process," said the Supervisor of Elections Mohammed Saneem.