They have started a petition against the proposal, which they claim would see nine and 10-year-olds sharing classrooms and toilets with teenagers.
Bro Idris will open as a school for three to 16-year-olds on six sites in Dolgellau from next September.
A Gwynedd council spokesperson said they aim to "listen to parents".
The secondary site will be at the present Ysgol y Gader site in Dolgellau, while the primary sites will be at Llanelltyd, Fairbourne, Dolgellau, Dinas Mawddwy and Rhydymain.
Ganllwyd and Brithdir primary schools will close as part of the plan.
Parents told BBC Radio Cymru's Post Cyntaf they thought primary education on the five sites would be only be for three to 11-year-olds.
But Gwynedd council said they are considering a plan to split pupils into three groups; three to nine-years-old; nine to 13-years-old; and 13 to 16-years-old.
Aranwen Manzini Hughes, a parent and governor at Ysgol Ieuan Gwynedd in Rhydymain, said the plan was not part of the original consultation process.
She added that parents were worried about primary age children having to travel to Dolgellau with older children.
A Gwynedd council spokesperson said a public engagement exercise was being held, including some drop-in sessions with parents.
They added: "The aim of the exercise is to update parents on the project's progress so far, introducing a possible education model that has been developed by the headteacher and shadow governing body as a starting point to stimulate debate and to listen and receive feedback from parents.
"Work is progressing well on the Ysgol Bro Idris project, with improvements completed to the building at the Ieuan Gwynedd site in Rhydymain and good progress made on the work at the Llanelltyd and Cynradd Dolgellau sites."
Parents have said they are "totally against" a plan to move primary pupils to a new secondary school in Gwynedd.