Fiji's president, Ratu Josefa Iloilo, and the military commander have met to discuss allegations that Commodore Bainimarama had plotted to overthrow the Qarase government.
The Daily Post reports that this has been confirmed by the president's official secretary, Paula Kunabuli, who says the meeting took place last Friday.
Mr Kunabuli says the two met regarding the commission of inquiry into allegations against Commodore Bainimarama but would not comment further.
However, the Post quotes reliable sources as saying the president is believed to be "reconsidering" the government's decision to set up a commission of inquiry.
The sources are reported as saying that as commander-in-chief, the president would have the last say.
A radio report this morning said President Iloilo and Commodore Bainimarama are expected to meet again on the issue soon.
Government officials pressed for an inquiry after three suspended senior officers alleged that Commodore Bainimarama planned to overthrow the Qarase government if his term as commander was not renewed.