Graham Martin, head teacher at Winwick CE Primary School has been suspended from his duties.
Pinaki Ghoshal, assistant director of improvement and school inclusion at the the borough council said: "The head teacher of Winwick CE Primary has been suspended by the board of governors to allow an investigation into allegations received to take place.
"This decision has the full support of both Warrington Borough Council and the Liverpool Diocese. Interim arrangements have been made to ensure the school operates as normal and that disruption to pupils is kept to a minimum."
No details of the nature of the allegations have been revealed.