Jane Bailey, the headteacher at South Shore Academy, has been suspended on full pay, the trust that runs the school has confirmed.
Bright Futures Educational Trust said the move would 'allow for an effective and efficient investigation to take place into issues around the management of the school'.
Her deputy, Neil Reynolds, has taken charge in her absence, with support from Ruth Coupe, the head at Marton Primary Academy, also run by Bright Futures.
Chief executive officer, Dr John Stephens, said in a statement: "We have suspended Ms Bailey from her duties as principal so that we can carry out a thorough and fair investigation into some issues that have been highlighted to us.
"As always, our decisions are taken in the best interests of the children, families and communities that we serve in South Shore as well as the Academy’s staff. We aim to conclude this matter as soon as possible.”
The trust's statement said Ms Bailey's suspension was 'an entirely neutral act and Ms Bailey will continue to be paid.'
Dr Stephens added: "We are continuing to invest heavily in the future of the staff and students of South Shore Academy.
"The move into the brand new, state of the art building will provide staff and students with the very best environment in which to teach, learn and continue to make progress."
A spokeswoman for Bright Futures said it was unable to comment further on the investigation, but said 'the suspension was not about safeguarding, but about issues around the management of the school in relation to day-to-day operations'.
More to follow.