Father Peter MacLeod-Miller of St Matthew's Church in Albury said he's personally buried trans individuals and is deeply worried the national debate and passing of the bill could put more children and adults at risk.

"It makes me ashamed to belong to religious institution," he said.

"I feel like an executive in a tobacco company."

Father MacLeod-Miller welcome the senate's decision to amend the motion to abolish the rights of schools to discriminate against gay or trans students.

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He is nonetheless "perplexed by the priorities of the government" and believes the debate and bill will lead to a harmful secrecy among gender diverse students.

"You need to ask who is going to bear cost of this?" he said. "It's going be most vulnerable people.

"Trans children and adults are already at risk and it says something really ugly about politicians that they're willing to make trans people collateral damage in the Prime Minister's legislative agenda."

Father MacLeod-Miller believes the bill is 'political payback' for the passage of the marriage equality bill.

"I can't understand why religious institutions are so focused on discrimination," he said.

"When you realise the genesis of the bill, it's not because vulnerable individuals are asking for greater protections. It's basically political payback.

"Any person with the slightest understanding of the marriage equality legislative journey would understand there's a trade off now, that passed and there was a promise to religious institutions that they would be given weapon for the future."