The initiative came from Whanganui DHB's funding and contracts manager, Steve Carey.
"Now the gender diverse community has access to the testing they need, when they need it, regardless of how they identify," Carey said.
"Not only does this enable better healthcare for those individuals, but it empowers them to be a participant in their own healthcare journey."
Pride Whanganui's Christina Emery, an advocate for the LGBTQ+ community, welcomed the move.
"When I read about the changes I was surprised this was even an issue - that we were being dictated to by a computer programme rather than using common sense," Emery said.
"But I am more than elated to know someone has flagged this and, more importantly, that an outcome has been reached.
"Any barrier for the transgender community is a barrier too many, so this is a step in the right direction. No one should feel they have to fight for basic healthcare based on who they are."