Justice Minister Andrew Little was surprised by Peters' talk of a referendum.
Peters said Little had not been blind-sided.
"If anyone got blind-sided, it was us. But we didn't get upset or have a hissy fit, as some do in politics," Peters told Sky News.
Ardern did not address the question when asked if Labour had acted in good faith, nor did she comment on whether New Zealand First had been blind-sided.
"I haven't seen the context of those comments, but people would have seen the process we've been engaged in," she told reporters this morning.
That process included Ardern campaigning on abortion law reform in 2017, a Law Commission report, and months of consultation with parties.
Ardern said there was nothing wrong with the abortion issue being absent from the Labour-NZ First coalition agreement.
"[The Abortion Legislation bill] shouldn't be characterised as a Government bill, therefore, you wouldn't expect it to be in an agreement. It's a bill that every MP will vote freely on.
"NZ First, it's up to them what they do. I take no grievance from taking different positions."
She said it was standard practice if a New Zealand First MP, or any MP, tried to amend the bill at the committee stage, such as adding a referendum clause.
"That's what we've seen already with the euthanasia debate, so it doesn't surprise me we've had those same suggestions for this bill."
This was not the first time Little had been surprised by New Zealand First, having had his plans to repeal the three strikes legislation scuppered last year.
Little suggested on Newstalk ZB this morning that Peters had initially given him a personal assurance of support to repeal the three strikes legislation.
"If you wanna go back a year or so, and I'd been in a situation of asking Winston Peters personally about something, which then a different outcome resulted."
He said he discussed the possibility of different referenda with New Zealand First last year.
"The issue came up, 'What about abortion?' and all the indications were that this wasn't going to be called for by anybody."
Asked if Peters had stiffed him, Little said people could characterise it how they wanted.
Ardern pushed back on any suggestion that Little and Peters didn't like each other.
"I wouldn't say that at all. Again, this is a bit of a different situation. We've tried to put a bill before Parliament that's not a Government bill and it has meant negotiating with different sides of the argument, including in the National Party, so it's not your usual piece of legislation."