The Fiji Army Commander Commodore Frank Bainimarama has identified senior civil servants to be the cause of opposition to the military's plans.
The differences first surfaced earlier last year when the government decided to reduce the sentences of soldiers involved in the 2000 mutiny.
Commodore Bainimarama says the government advisers should refrain from any of their sinister moves.
He says they are also trying to remove him from the helm of the military when his term expires next month.
Commodore Bainimarama has been vocal in his criticism of the way the perpatrators and those involved in the events of 2000 are being edorsed.
The acting permanent secretary of Home Affairs, Peni Lomaloma says they want a new Commander for the military who does not involve himself in politics.
Meanwhile, the government has directed the military to reduce its manpower by 336 regular soldiers as provided in the 2004 budget.
Commodore Bainimarama admits the army is overstaffed and is negotiating that his redundant soldiers be compensated.