The Fiji military says the lines of reporting between the commander, Commodore Bainimarama, and the minister and the president are being contested.
This follows reports that president Ratu Josefa Iloilo rejected a request from the home affairs minister, Josefa Vosanibola, to suspend the commander over insubordination and speaking publicly about his opposition to the Reconciliation bill.
The military spokesman, Captain Neumi Leweni, would not say whether an attempt at suspension had occurred but he did confirm that the president had met the commander.
Captain Leweni says there is some confusion as to where the lines of reporting begin and end.
"There are some, you could say, differences in opinion on how far the report goes in to the minister and to the president, so that's why I'm not in a position right now to say any more on the issue."
Captain Leweni would not explain how the issue was being contested and the Home Affairs minister was unavailable to comment.
Fiji's constitution states that the minister has executive authority over the military while the president is the military's commander-in-chief but there is little clarity on the roles.