Mrs Philippa Baker-Hogan said while she respected the views held by the petitioners, council needed to "stick to our knitting".
She said it was difficult to leave the meeting, particularly with a large group of people presenting their petition "but it's a long stretch to involve local government in this issue that is clearly the domain of central government".
"I believe our community wants us to stick to issues that directly affect us. That we can decide on and free trade agreements between countries just doesn't hit that threshold in my opinion.
"I've nothing against the people or their opinions, and I may even personally agree with them. But we have a responsibility to the wider community to be prudent with our time and resources and be very clear in the lines between local and central government responsibility," she said.
"It was raised with the Mayor in at least two forums that there may be a walk out or objection so no surprise a few of us left. But we all left of our own accord."
Mr Stevens said he stayed and listened to what the petitioners had to say.
There were two recommendations on the agenda and he said "I was happy with those" (They were that council receive the information and the petition).
"But when the Mayor recommended council accept the 12 resolutions in the petition that's when I left because I could not support them," he said.
"My question is why don't these people petition the local MPs and party candidates because this sort of thing has nothing to do with our council." He said there was no collusion among the councillors who boycotted the meeting "but if it comes back to council, my position will not change".
Mrs Craig left the meeting before the item was discussed and said there had been no collusion among councillors involved.
"Each councillor made a personal decision to not attend this session and had made no calculations as to the final result being the loss of a quorum," she said.
She said she absented herself from that part of the meeting on a matter of principle and it was not an decision taken lightly.
"The Mayor was aware there were a number of councillors who did not believe this item should have been on the agenda and yet still went ahead, leading to an unfair expectation from the TPPA group.
"We are paid to govern at a local level, and if our attention is constantly taken up by special interest groups who want to protest on central government responsibilities, we'll be there all day, every day. That is not what our ratepayers pay us for."
She said while council makes submissions to Government when it was appropriate it could not be used as a political tool for every special interest group who has an issue. "Chester Borrows is our local MP and this group should be lobbying him as their Government representative."
The petition is part of a national campaign against the proposed trade pact and concerned about the secrecy surrounding the deal and ramifications such as more liberal rules on foreign investment, giving overseas companies the right to sue the Government over claimed lost investment value, and more expensive medicines, .
Mr Vinsen earlier told the Chronicle yesterday he did not believe the matter was council business.
The submitters went to council because, under the Local Government Act 2002, they believe it has a "duty to protect its citizens".
