Deputy secretary sector enablement and support Katrina Casey said the ministry had been told four board members had resigned.
"Along with the New Zealand Trustees Association, we are working closely with the school's board and leadership to support effective school governance, school operations and the delivery of the New Zealand Curriculum," she said.
"The process to replace the board members who have resigned will now begin."
Another Ministry of Education spokesperson said three people remained on the board.
The Herald has approached the school principal, who remains on the board, for comment.
Whenuapai School, which caters for children in Years 1 to 8, is located on Airport Rd.
According to its website, it was first proposed in 1957 when the Waitemata City Council decided to build a new school.