The Assembly of Christian Churches in Fiji says the military commander, Commodore Bainimarama, is a threat to national security and reconciliation.
The Daily Post reports that the churches have written to President Iloilo asking him to discipline Commodore Bainimarama.
They have told President Iloilo that it is his God-given assignment to bring about reconciliation, and stressed that it is time for him to act and control the commander.
In their letter, the churches say the commander's recent outbursts are "causing instability and insecurity among church members" who fear that "he wants to bring about military rule."
The letter has been signed by the chairman of the Assembly and senior Methodist church official, the Rev Tuikilakila Waqairatu, and five other leaders of mainly newer churches.