The opening of the new £11.5m primary school in Llandudno Junction has been delayed by at least six months.
The 492-pupil Ysgol Awel y Mynydd in Esgyryn was due to open on 1 September.
But "difficulties negotiating the purchase of land" and "poor winter weather" have delayed pupils moving in until at least Easter 2017.
Conwy county councillors are concerned about siblings being educated apart, disruption and a lack of communication.
The new primary school will merge Ysgol Nant y Coed and Ysgol Maelgwn primary schools.
Now the council is considering whether to keep both schools open until the new school is ready - or split three to seven-year-olds and seven to 11-year-olds between the two sites.
Ysgol Awel y Mynydd temporary board governors said they would prefer to split younger and older age groups between the two sites.
A consultation has been launched with parents and a special meeting of the cabinet will meet on 28 June.