On Thursday, a group of Indigenous campaigners lodged a petition in the Legislative Assembly that said the sanctity of marriage involved a man and a woman and any change to allow same-sex couples to marry would be an "affront to Aboriginal people of Australia".

The petition, signed by six people, called on the Assembly "to reject any attempt to redefine the institution of marriage, and in doing so, honour the sanctity of both the tradition of marriage and the spiritual implication of this sacred union".

The view is not held by all Aboriginal and Torres Strait Islander leaders.

The petition was lodged formally by opposition Indigenous affairs spokesman Andrew Wall, who is opposed to marriage equality. No government member was prepared to lodge the petition, which comes after the current Assembly voted in favour of the territory's own same-sex marriage laws in 2013, later overturned by the High Court.

Mrs Jones, a conservative Catholic opposed to equality for same-sex attracted Australians, later agreed to escort members of the group into the private areas of the Legislative Assembly building, including to ministerial offices.

Once there, they presented copies of the petition and held prayers for members of the Assembly who support the reform. Mrs Jones was called to vote in a division in the Assembly chamber and left the group with a member of her staff.

Mr Barr told an adjournment debate the group had arrived in his office "without any invitation, without any expectation of their arrival" and in breach of security protocols for members' guests.

The group prayed for Mr Barr, who is a prominent supporter of same-sex marriage and in a long-term relationship with his partner, Anthony Toms.

In a statement on Friday, Mrs Jones said she was unaware of the rules about guests inside the Assembly and said members of the group asked for permission to pray in each office.

"The Indigenous visitors came from across Australia and were humbled to be at the Assembly," Mrs Jones said. "The event brought some of them to tears on numerous occasions. However, I should have been more understanding of the members and staff."

On Friday, Mr Barr said he was concerned about the protest, but accepted apologies from Mrs Jones and Opposition Leader Jeremy Hanson.

"My position on marriage equality is well known," he said. "I don't need a prayer group arriving unannounced in my office to pray for me. Regardless of the intent there, it couldn't be interpreted any other way than as an unfriendly approach.

"I am not changing my mind on that issue. It doesn't matter who prays for me."

Mr Barr declared the matter closed.

Speaker Vicki Dunne's office said discussion about security in the Legislative Assembly was subject to ongoing review.