Plans for the Ysgol y Berwyn site were originally approved in 2015, and the campus was due to open in 2018.
But a petition called for a review of proposals that would see the Church own the buildings.
On Tuesday, Gwynedd's cabinet agreed to consult on the school's Church status.
The Diocese of St Asaph said it was "disappointed but not surprised" by the decision, and accused the council of making "a complete mess of this project".
"The fundamental issue here is that Cyngor Gwynedd (council) has withdrawn its support for this project and as a result has intentionally destabilised the partnership," said the Church in a statement.
The original plans would have seen the merging of Ysgol Bro Tegid and Ysgol Beuno Sant, a Church in Wales school, with the secondary Ysgol y Berwyn.
But following calls for the site to be designated a community campus - rather than a Church school - the council cabinet has agreed to a new formal consultation.
"Unfortunately, following a long period of working in partnership with the Church in Wales, the latest developments have caused great concern amongst governors and members of the local community and poses a significant risk to the success of the school," said the cabinet's education member, Gareth Thomas.
"As a result, the cabinet has decided to support the recommendation to hold a formal consultation with governors on the option to abandon the existing proposal."
In its statement, the Church said it felt the council "now has a responsibility to the community, children and the diocese to find a way forward that develops community and church education".
Church officials said they hoped the council would contact them over the developments "as a matter of urgency".
Gwynedd's council leadership has come under fire from the Church in Wales in a row over the future of plans for a new £10m school campus serving the Bala area.