Fiji's police commissioner, Andrew Hughes, says the public row between the military commander and some public servants is an internal matter.
Radio Fiji quotes Mr Hughes as saying he does not see any threat to national security as yet.
Commodore Bainimarama wants two more former military officers who currently hold senior posts in the Home Affairs Ministry removed.
They are Benjamin Lomaloma and Lesi Korovavala who, the military commander says, are a threat to national security.
And he says the head of the Prime Minister's office, Jioji Kotobalavu, is just as big a threat and must go.
But Mr Hughes says the matter is not for the police to look into.
Earlier, the former Prime Minister who seized control of the army after his 1987 coup, Sitiveni Rabuka, had said that if Commodore Bainimarama had any proof of a threat to national security, then the matter should be reported to police.
Yesterday, the Prime Minister intervened and told the Home Affairs Minister to have discussions with the military commander and settle the row.