Former deputy prime minister Barnaby Joyce has called for private schools to retain the right to ban or expel transgender children to stop them from going into single-sex change rooms and bathrooms.

The former Nationals leader raised the example of sending his children to an all-girls’ school, only to discover a child who was born a boy was using the same toilets.

His comments have sparked anger among the families of trans children, who have urged Mr Joyce to sit down and talk to the children affected.

Mr Joyce said any legislation to stop discrimination against lesbian, gay, transgender and intersex students must not stop schools from banning or expelling trans kids.

“If I send my child to an all-girls’ school, I don’t want the complication and the possibility, and they haven’t completely ruled it out, that if someone turns up and says, ‘I want to identify was a woman, I want to identify as a girl, I want to go Into your bathrooms, I want to go into your change rooms, I want to be educated’,’’ Mr Joyce said.

“That might be that person’s right and wish, but everybody else says, ‘well that’s an affront on our rights’ and we want that issue deal with. We want it dealt with clearly so that we know that our rights are protected and other people’s rights are respected,” he said.

“You cannot send a student whose genetic make up is XY … to a school established for people who are XX. It is not fair on the larger school unit that they have to change and accept all because of the desires of one.”

Mr Joyce’s comments have sparked outrage among families with trans children, with angry parents calling for him to resign.

Jo Hirst, a former primary school teacher, is the mother of two sons, including one who is transgender. She is the author of The Gender Fairy, a book for parents and teachers to help transgender children feel normal and know they are not alone.

“Barnaby Joyce has shown zero understanding or compassion for transgender students,” Ms Hirst told The New Daily.

“When a parent and a school support a trans child, it is on the advice of that child’s doctors and psychologists.

“We are doing what is in the best interest of that child’s academic and mental health outcomes.  Many faith-based and independent schools understand this and are doing a great job of supporting transgender students,” she said.

“When we have a federal minister blatantly flouting the recommendations of our health professionals, and publicly shaming and disparaging our vulnerable kids, I think it’s time for our Prime Minister to step in and say enough is enough.

“These children deserve better than this. He should be asked for his resignation.”

Rainbow Families Victoria director Felicity Marlowe said parents were deeply saddened by the remarks.

“There’s a real lack of empathy and understanding abut the day-to-day impact of discrimination against trans kids,’’ Ms Marlowe said.

“We can’t continue to have people … peddle so much misinformation – it’s so damaging!

“I would urge Barnaby Joyce to meet with some parents of children in faith based schools.”

Deputy Prime Minister Michael McCormack said he did not agree with Mr Joyce’s remarks.

“I don’t want to see any child discriminated against and, quite frankly, I think what Scott Morrison has put forward means that no child will be discriminated against,’’ he told Sky News.

Mr McCormack has previously been forced to apologise for his 1993 comments that homosexuality was “sordid” and “unnatural”. The comments were made in a newspaper editorial.

“Unfortunately, gays are here and, if the disease their unnatural acts helped spread don’t wipe out humanity, they are here to stay,’’ Mr McCormack wrote.

The Nationals leader has subsequently apologised, saying he had “grown and learnt not only to tolerate, but to accept all people, regardless of their sexual orientation”.

Mr Morrison pledged during the Wentworth by-election to pass new laws to protect lesbian, gay and transgender kids before Christmas.

However, this week he announced the Coalition could not reach agreement with Labor to pass the laws.