The acting principal of St Kevin's College has been forced to step aside less than 24 hours after being promoted to the position, due to an allegation that she pressured a former school counsellor not to report a grooming allegation involving a teacher and a schoolboy.

School parents were already reeling from the news, revealed by the ABC, that the school's headmaster and sports dean had given references to volunteer athletics coach Peter Kehoe, who was convicted of grooming year 9 student Paris Street in 2015.

The Catholic school's governing body, Edmund Rice Education Australia, also announced a shake-up of the college board on Thursday, appointing a new chairman Paul O'Malley, in an attempt to rebuild the school's reputation in the wake of the fallout from the Four Corners expose.

These changes came the day after the school's headmaster Stephen Russell resigned over his handling of the case and the dean of sport, Luke Travers, who staunchly defended former volunteer coach and convicted child groomer Peter Kehoe, was formally stood down.

John Crowley, former principal of St Patrick's College in Ballarat, replaced Mr Russell as headmaster of the college on Thursday.