Justice Minister Andrew Little is disappointed that proposed "safe zones" around abortion clinics got axed late last night in a voting mix-up.

But Prime Minister Jacinda Ardern, who supported the proposal to establish 150m protest-free areas around clinics, has brushed off the error as "the outcome of democracy".

An amendment to scrap the safe zones, in the name of Act leader David Seymour, was split into two parts during the committee stage of the Abortion Legislation Bill late last night.

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The first part of the bill was voted down 59 votes to 56 in a conscience vote, but the second substantive part - which effectively scrapped the proposed safe zones - passed with a voice vote were MPs voted vocally and the Speaker ruled which side had won.

If any MP had asked for a personal vote, then individual votes would have been tallied and given the result for the first part of the amendment, the second part seems likely to have been voted down too.

After the vote Green MP Jan Logie, who supports safe zones, sought to clarify what had happened, and Labour MP Ruth Dyson then unsuccessfully moved for a personal vote to be taken; only one MP needed to object to defeat Dyson's motion.

An amendment to the Abortion Legislation Bill has axed safe zones which would protect women from anti-abortion protesters outside clinics.
An amendment to the Abortion Legislation Bill has axed safe zones which would protect women from anti-abortion protesters outside clinics.

Supporters of safe zones said they protected women seeking abortions from harassment, intimidation and attempts to breach their medical privacy, but opponents said there were already such protections in existing law and the zones would have infringed on freedom of expression.

Little, who couldn't call for a personal vote as it was his bill, said he was disappointed other MPs didn't call for the vote.

And women seeking abortions are entitled to be disappointed as well, he said.

"As the author of the bill, I put it in there because I thought it was important to have that available to us where a need was apparent.

"It's not in the Bill, that is disappointing but I'm very pleased that everything else in the bill that came under pretty fierce attack last night is still there."

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National MP Nikki Kaye, who supports safe zones but was not in the House when the vote was taken, said: "I'm really, really gutted."

Ardern said she would have preferred those protest-free areas were in place but brushed off questions about who was to blame.

"There is no blame here, this was simply the outcome of democracy and process."

She said it was more important that the main parts of the bill were unchanged, which would see abortion taken out of the Crimes Act and an end to the statutory test for the procedure for pregnancies less than 20 weeks.

Little said he won't try to re-insert protest-free zones into the bill as he isn't confident enough on the numbers.

And there were other laws available to police to stop harassment, he said.

Meanwhile, Seymour is just pleased his amendment passed and the safe zones are gone - no matter if it happened by mistake.

"I happen to think we got the right outcome.

"I hate these odious ogres who stand outside abortion clinics but I also didn't come to Parliament to make laws allowing ministers to ban free speech in whole areas."