The Charity Commission said it was not satisfied that the safeguarding policies, procedures and practices of the two charities - Ampleforth Abbey Trust and the St Laurence Education Trust - were "adequate and working properly."
The Commssion's concerns about compliance are being investigated by North Yorkshire Police and there is also a review by North Yorkshire County Council.
The move comes 16 months after the watchdog opened a statutory inquiry into the charities to investigate their approach to safeguarding and handling of allegations of abuse at the independent Roman Catholic school, near Helmsley.
The Benedictine monk-run institution has been dogged by sexual allegations against former teachers.
In the most recent case, in March last year, internationally-renowned musician Dara De Cogan was jailed for 28 months for sexual offences against a female pupil.
De Cogan, 58, groomed and sexually exploited the girl between 2007 and 2009 while working as a music teacher at the college.
In 2015 David Lowe, a former housemaster at the college, was jailed for 10 years for sexually abusing boys at two schools as they slept in their dormitory beds and during singing lessons.
The interim manager Emma Moody, a partner in Leeds-based law firm Womble Bond Dickinson "will have all the powers and duties of a trustee, to the exclusion of the trustees, in respect of a number of safeguarding related matters", the Charity Commission said.
It comes after the Commission reviewed the progress made by trustees in implementing recommendations from an independent review last March.
Harvey Grenville, Head of Investigations and Enforcement at the Charity Commission said: "We are not satisfied that the trustees of these charities have made enough progress in improving the safeguarding environment for pupils in the schools connected to the charities.
"For this reason, we have appointed an interim manager to expedite changes in the safeguarding arrangements at the schools."
A North Yorkshire Police spokeswoman said: “The North Yorkshire Safeguarding Children Board, which includes North Yorkshire Police and North Yorkshire County Council, are aware of the Charity Commission’s appointment of an interim manager and support this action.
“North Yorkshire Police is currently investigating the concerns referred to by the Commission relating to the school’s compliance with safeguarding measures, and this is also subject to review by the Local Authority Designated Officer.”
On its website Ampleforth College said the appointment was a "precautionary measure."
In a statement it added: "“The safeguarding of children and adults is paramount in all the works of the Ampleforth Abbey Trust and the St Laurence Education Trust.
"We welcome the insight which Emma Moody and her team will bring to Ampleforth, and are committed to working with them to implement their recommendations regarding governance in relation to safeguarding."
They also repeated "sincere and heartfelt" apologies to anyone who had "suffered harm" in Ampleforth's care, giving telephone numbers to ring at the college and the charity Survive.