The issue of including pupils identifying as transgender in single-sex spaces has been described as a “minefield” by a Government minister.

In an inquiry from the Commons’ education select committee into Government support for children in children’s homes, Will Quince, Minister for Children and Families, said he would “probably wouldn’t be overly happy” for his daughters to share a boarding house with a pupil identifying as a trans girl.

Caroline Johnson MP said the number of children identifying as transgender was increasing, and that “schools need to strike a balance of ensuring that these children can be cared for properly and that their needs are properly met”.

She added that schools needed to balance this with the needs of the wider school population, and said she had been contacted by parents with concerns about an 18-year-old trans girl sharing a boarding house with their daughters.

She asked what guidance the Department for Education could give to schools to manage including trans pupils in single-sex spaces.

Mr Quince said the issue was a “bit of a minefield” and that the Department for Education was working with the Government Equalities Office to create guidance.

He added that the school referenced was a private school, which made this “slightly more complex”.

He said there were two “competing priorities”, the 2010 Equalities Act and the importance of treating young people equally, and the school’s “legal obligations, a duty to safeguard and protect and promote the welfare of all children”.

“And on the face of what you’ve just said, as a parent and particularly a parent of two young girls I probably wouldn’t be overly happy with the situation you’ve described,” he added, suggesting the concerned parent speak with the head, governors or Independent Schools Inspectorate.

He said he would speak to the Schools Minister about forming more guidance but that schools needed to use “their common sense and follow the law as it stands as the moment, and I would suggest that the duty to protect and to safeguard should probably override anything else”.

He said the “number one priority” of schools should be the safeguarding of pupils.

Elsewhere in the session Mr Quince said that the Government needed to make sure that schools had no “perverse incentive” to put off pupils with special educational needs from applying, adding that the Send review would be published this month.

Asked if he had made a case for extra-curricular activities being included as part of a longer school day to the Department, Mr Quince said he “could certainly” explore a pilot of the idea.

“You’re preaching to the choir when you talk about extra-curricular activities, sport and music and drama and all sorts of other clubs and societies around a whole-school approach to mental wellbeing,” he said to committee chairman Robert Halfon.

He added that he would not commit to piloting longer school hours until he had discussed this with the department.

Mr Quince said in the session that childhood obesity and obesity was one of the “biggest issues faced by the country”.

He said the mandatory RSHE curriculum over healthy food would help with this and said he had met with chef Jamie Oliver to discuss school food standards on Monday.

A spokesperson for the transgender children’s charity Mermaids said: “At Mermaids we hear of many schools who do a wonderful job supporting gender-diverse pupils who are simply trying to focus on their education.

“The small number of schools that are using financial resources and staff time to organise a blanket ban on trans pupils attending single sex schools is really sad and perplexing – can we think of another marginalised population of young people where this happens?

“At the heart of this is a young person who wants to learn, as themselves – it’s actually very simple when you think of it like that.

“We look back in history and can recall gender being a reason access was denied to girls and now we have that institution denying access to another marginalised group of learners. When will we learn?”