Sources say Bainimarama has given the President of the Methodist Church, Reverend Ame Tugaue, and General Secretary, Reverend Tuikilakila Waqairatu, as well Reverend Manasa Lasaro until noon today to step down.
They say the trio have been told not to attend the meeting and he wants an interim chair of his choice to preside over the conference.
Sources say Bainimarama has his own nominations for the Presidency and Secretary General.
They say the Church is firm in its resolve not to bow down to the dictator's request and intimidating tactics.
The military team have also requested the Methodist Church to endorse the People's Charter on the first day of the conference otherwise they will cancel the rest of the conference.
Coupfourpointfive last week revealed key Methodist Church leaders were being taken in and being spoken to by the military junta, worried they might be 'making trouble' at its conference.
Ministers were being grilled about the conference, its agenda and possible protests.
It was also urging the Methodist Church to 'promote unity and equality' with military spokesperson Colonel Neumi Leweni telling Fiji Village 'the RFMF has been reliably informed that there are elements within the church that have been planning to utilize the upcoming church conference to instigate instability.'
He said "the law will take its course if a member or delegate of the Methodist Church of Fiji conference engages in any unlawful activities".
Leweni said the church Secretary has been told the meeting will be cancelled if members deviate from the original agenda.
It looks like the military dictatorship is extremely rattled by the thought of the Methodist Church, which along with the GCC, media and now unions, it has tried to crush so it can continue to run Fiji unelected, meeting next week for the first time since conferences were cancelled in 2007.