Speaker Robyn Lambley stepped down from the chair to submit the petition on behalf of the Australian Christian Lobby that "prays... all medical and surgical transitioning treatments for children in the Northern Territory," be suspended to "protect them from further injury".
Ms Lambley was brief in her submissions on Thursday simply stating the petition, with 463 signatures, met parliamentary requirements.
It also called for an independent review into gender-affirming care.
During the August election campaign the ACL took out several half-page advertisements comparing candidates against their religious values.
It gave all Country Liberal Party candidates and two independents, including Ms Lambley, a tick for supporting a review into medical and surgical care of gender-diverse children.
However, for territory transgender man Elliot Hughes, who said he first knew he was transgender when he was four years old, the politicisation of his healthcare felt dehumanising.
"I think children need to be protected and supported," he said.
NT Speaker Robyn Lambley tabled a petition to suspend access to gender-affirming care for children. ((A)manda Parkinson/AAP PHOTOS)
"This all goes against that for some kind of ideological argument about what it is to be a man or what it is to be a woman."
Mr Hughes said it further demonised the LGBTQIA+ community which over decades had been subjected to harmful politicisation by conservative governments and groups.
"It becomes this conflict, where we're always having to fight for the bare minimum, and that doesn't give us space to thrive, to excel, or to contribute to our full potential," he said.
Top End pride chairperson David Toro said for many in the community gender-affirming care was not optional, dismissible, or removable, but essential.
"Denying access risks deepening stigma and marginalisation, and we vehemently condemn this [petition]," he said.
Petition signatory and former independent MP Mark Turner, however, said he believed gender services needed to be better regulated.
"What concerns me is, we are progressing towards a laissez-faire, capitalistic health system...that could lead to absolutely tragic and preventable outcomes," he said.
"We've got bad actors who are just pumping [prescriptions] out for profit as much as they can... just to make a quick buck."
But existing high court precedence already safeguards a child's access to care, NT Anti-Discrimination Commissioner Jeswynn Yogaratnam said.
"The High Court has also decided in Kelvin, 2018, that medical practitioners must meet specific requirements for gender-affirming treatment of minors," he said
"The best interests of an individual child should be at the centre of decision-making, and a blanket suspension of treatment does not seem appropriate or necessary."
Transcend Australia executive officer Jeremy Wiggins said local and global evidence showed access to care benefitted young people's mental health.
"The thousands of families we support deserve to know that their healthcare will continue," he said.
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