The action was taken by St Columba's School in Inverclyde after details of police investigations came to light.
Police Scotland confirmed that it was investigating a recent allegation involving a young child.
A 56-year-old man has also been reported to prosecutors over alleged historical abuse of a 15-year-old girl.
A Police Scotland spokeswoman said: "We can confirm that a complaint has been received regarding a sexual assault on a young girl.
"Enquires are ongoing to establish the full circumstances and it would be inappropriate to comment further at this time."
On the other allegation she said: "A 56-year-old man has been reported to the Procurator Fiscal in connection with non-recent alleged sexual abuse of a 15-year-old girl."
The co-educational school, based in Kilmacolm, caters for about 700 pupils, with annual fees of about Â£11,000.

The engineering firm says the £250m expansion of its Malmesbury headquarters will eventually bring 3,000 new jobs to the town.
Planning conditions have been added regarding archaeological issues and addressing site access, along with concerns about increased traffic.
The expansion is expected to be the largest in the firm's 20-year history.
A spokesperson for Dyson said the decision was just one part of a number of stages in the planning process and they did not want to comment further.

LL Camps in Bushey, Hertfordshire, was closed by Ofsted last week and director Ben Lewis has been charged with possessing indecent images of children.
Following the closure, parents vented their anger on the firm's Facebook page at the initial lack of information.
But camp co-founder Tal Landsman has now said refunds will be issued.
Ofsted closed the camp on 6 August and the company's website was taken down soon after.
One parent whose child was due to attend the US-style day camp wrote it was an "utter disgrace".
Another was concerned about parents who "could not afford alternative care without the refund".
A man whose children had gone to the camp told the BBC: "Fortunately, for us they were only going for one further day, and then they were going to a different camp.
"Had it been the situation that they were due to be there this week and all of next week, we'd be in a bit of bother."
But on Wednesday, Mr Landsman confirmed parents would be able to fill in a refund form which has been placed on a holding page on the company's official website.
Mr Lewis and Mr Landsman opened the holiday club in 2010.
Two teachers at one of Scotland's leading private schools have been suspended amid separate allegations of sexual abuse of young girls.
[NEXT_CONCEPT]
Outline plans to double the size of Dyson's research centre in Wiltshire have been approved by planners.
[NEXT_CONCEPT]
Parents of children due to go to a summer camp whose director has been charged with possession of indecent images have been offered refunds.