Fiji government senator, Mohammed Apisai Tora, has denied asking the military commander to oust President Iloilo just a week after he had taken office during the Speight coup.
Commodore Bainimarama said last week the request to oust the president was put to him in the boardroom of Fijian Holdings Limited as the post coup interim administration was being appointed in 2000.
But Mr Tora has told the senate that he was never part of any such plot.
The Fiji Times quotes Mr Tora as saying he is grateful the story has been highlighted because the "real people" behind the coup will be investigated.
Senator Tora has called for the resignation of Commodore Bainimarama and asked him to co-operate with police in investigating into the allegation.
But a military spokesman, Captain Neumi Leweni, says the request to oust the president was put to Commodore Bainimarama personally and he stands by his statement.
He says the military knows how to deal the likes of Mr Tora and is keeping a watch on him.