Commodore Voreqe Bainimarama says the military will resist any attempts to destabilise it or thwart its clean-up campaign.
Speaking on a Fijian radio station talk-back show, he named individuals who he said they were monitoring because they were inciting civil unrest.
He warned people and non-government activists, including Fiji Women's Rights Movement executive director Virisila Buadromo, human right activist Patricia Jalal, businessman Imraz Iqbal and businesswoman Laisa Digitaki to stop saying things that could incite unrest.
Commodore Bainimarama said these individuals blamed the military for a fire in Lami last week.
He said the military had nothing to do with it. He said the individuals he had named should shut their mouths or else the military would shut it for them.
He said people should not forget the deaths that had occurred in Queen Elizabeth Barracks on November 2, 2000.
He warned people against civil disobedience, saying the military would look into it seriously.
Commodore Bainimarama said Ms Buadromo and Ms Jalal had placed his mobile number and email address in the newspaper for everyone to use and it was causing problems for him.
He said on Wednesday night, he was informed of the outcome of the Great Council of Chiefs meeting and that the chiefs were told that since the military did not want to be part of the meeting, the chiefs were reminded that this was their land and their people.
He warned people not to be misled by their chiefs because some of them had their own political agenda and would gain in such circumstances.
Commodore Bainimarama said the military would not tolerate any individual or group that would want to destabilise and be a hindrance to its clean-up campaign.
Ms Buadromo said the warning by Commodore Bainimarama was really scary as it was done on a national radio station.
"Why us, we do not have any guns? We are only using words. We have not broken any laws," she said.
She said truth would always prevail at the end of the day.