Gwynedd council decided to go ahead with establishing a new Church in Wales campus at Ysgol y Berwyn in Bala.
Governors want it designated as a community site and 500 people have signed a petition against the move.
The council spokesman said it had received the objections and would "carefully consider the contents of the letter".
The plan would see the merging of Ysgol Bro Tegid and Ysgol Beuno Sant, a Church in Wales school, with the secondary Ysgol y Berwyn.
In December, the council alleged the church no longer supported the project, something it denied.
Chairman of governors Gwion Lynch said following this row, it confirmed fears the relationship would not work and any trust had been shattered.
The Church in Wales said only two of the 17 places on the shadow governing body would be for its members, with two others reserved for other Christian traditions in Bala and the remaining 13 places would be for others - religious or not.
A spokesman said the church remained "fully committed to providing the best educational opportunities for the children and young people of Bala, Penllyn and surrounding areas".
A report is expected to be discussed at the council's cabinet meeting on 14 February.
If all goes to plan - the new three-to-19 campus will open in September 2018.
Governors at a Gwynedd school want a consultation restarted over church ownership of its new £10m campus.