Ms Shannon said the ministry was confident the school could continue to deliver quality learning for its students while the work was under way.
It was understood deputy principal Lesley Smith would become acting principal following Mr Shortcliffe's resignation, she said.
The Hastings Intermediate School board of trustees is maintaining that its focus is on the success and achievement of its pupils.
Board chairperson Jo MacDonald said the board of trustees invited the ministry to come into the school and help provide support and mentoring.
"Moving forward, the board of trustees' focus is on the success and achievement of all 445 of our students, their welfare and that of the staff and community," she said.
Mr Shortcliffe was due to take up a new principal role at Fairfield Intermediate School on October 10, and did not respond to a request for comment.
Fairfield Intermediate board of trustees chairperson Jo Blaikie confirmed Mr Shortcliffe would be starting on that date and said she felt "absolutely comfortable" about his appointment.