A Canberra Liberals politician says the Safe Schools program has "made schools harmful" by traumatising students, damaging their innocence and asking them to sexually fantasise about their own gender.

Opposition youth spokeswoman Elizabeth Kikkert made the comments after her colleague Andrew Wall tabled a petition in the ACT Legislative Assembly, pushing for the withdrawal of government support for the program. The petition had garnered nearly 1,000 signatures.

Ms Kikkert said she had spoken to Canberra children who left school crying after being taught material from the program, which was designed to support and reduce bullying rates among LGBTIQ students and staff.

She said the children were "so upset that they could not sleep for several nights" and that they "have refused to return to their classes because they feel unsafe there".

She then claimed teachers were asking 13-year-old female students to fantasise about other girls.

"This is overt sexualisation. One could even accurately call it grooming," she said.

"Requiring young people to experiment with sexual attraction of any kind has no place in our classrooms."

Ms Kikkert said one student confessed the material made their "mind uncomfortable".

She said the decision to establish a program that supports only sexually and gender diverse students was neglecting other "vulnerable" groups who were not adequately supported, including Aboriginal and Torres Strait Islander students.

"There are many reasons why a student might be bullied at school," she said.

"Some might be bullied because they do not seem smart, others might be bullied because they are too smart or socially awkward.

"I call on this Government to broaden its scope so we can make our schools safe and supportive for all vulnerable youth."

When tabling the petition, Canberra Liberal Education spokesman Mr Wall said he had "severe concerns" about the program being rolled out in ACT schools.

Earlier this year the ACT Education Directorate allocated up to $100,000 of funding for the controversial initiative.

Labor and Greens slam petition

Both of the ACT's other major political parties condemned the petition.

Education Minister Yvette Berry said she was deeply saddened and appalled by the move, though not surprised.

"I think Mr Wall should be ashamed of himself," Ms Berry said.

"What this petition says, Madam Speaker, to LGBTIQ kids - [is] 'there is something wrong with you, you are not welcome in our schools and you are not supported in our communities'."

She said she was sure Mr Wall had been clear about his own sexuality his whole life but that tabling the petition showed he was not prepared to help children who had not been.

Greens MLA Caroline Le Couteur criticised both the contents and timing of the petition, given LGBTIQ people were already having their sexual orientation scrutinised by national debate as the same-sex marriage postal survey approaches.

"This should not be a political issue, it is a human issue," Ms Le Couteur said.

"It is the lack of acceptance and legitimacy of being same-sex attracted, intersex or gender diverse, that simply perpetuates the harm and discrimination that these young people feel and experience.

"And this is what leads to the increased prevalence of mental health issues among these young people."