Early childhood services want more evidence it will be safe to reopen next week and some are likely to remain closed.
The government said schools and early learning centres can reopen on 29 April for children who cannot learn from home or whose parents are going back to work at alert level 3.
It said children and teenagers were at low risk of catching and passing on the coronavirus.
The Early Childhood Council, which represents more than 1000 early childhood services, had called for centres to remain closed until the country reached alert level 2.
The council's chief executive, Peter Reynolds, said he was disappointed the government did not heed its call.
"The government has heard that we're concerned and they've chosen to ignore and that's deeply disturbing," he said.
"We would hope that centres see sense with this. If they have any level of discomfort with the issue at all or their staff have a level of discomfort, then they'll choose the sensible path forward and not reopen at this moment."
Reynolds said the government needed to provide the evidence that it was safe for early learning services to reopen.
Reynolds told Morning Report that social distancing among young children would be impossible and he was worried a centre could be the source of the next Covid-19 cluster.
Some centres may not reopen, he said, which would create difficulties for parents needing to return to work.
The chief executive of Te Rito Maioha Early Childhood New Zealand, Kathy Wolfe, said its 500 centre members appeared to be evenly divided over whether to accept children back at level 3.
"It varies from members who are really nervous about opening and feel the risk is really high to open, to others who absolutely understand that they are there to support parents who return to work," she said.
Director-General of Health Dr Ashley Bloomfield told Morning Report he understood there would be concerns, but just like they had worked out ways to keep essential workers safe, the same applied to students and education staff.
"This is a setting that we've been really thoughtful about," he said, adding that experts had looked into overseas evidence.
"There's little evidence to show closing [schools] makes much of a contribution to reducing transmission.
"The key thing here is this evidence, which is quite consistent around the world and which we've seen here in New Zealand, is children and teens seem to be much less likely to be infected and if they are infected they are less likely to be affected, so they don't tend to have much in the way of symptoms and don't seem to transmit it on to adults."
However, Reynolds disputed those claims, saying the evidence they had seen overseas contradicted that.
"Up to 25 percent of cases could be asymptomatic, which means people don't even know they've got Covid-19. Kindergartens and primary school classes for younger children will remain closed as they can't observe social distancing - that's the reality for Germany, we're not sure why it's not the reality here."
He said he expected demand to be mixed, with some parents who will want to make use of facilities but others will be nervous and even staff not willing to put themselves at risk.
"A petition conducted recently had over 30,000 signatures on it from ECE teachers and staff who don't feel confident about returning at this time."
School principals react to level 3 news
School principals appeared to be happier about the decision.
The president of the Principals' Federation, Perry Rush, said they understood that schools needed to reopen so parents could get back to work.
"The prime minister set us a challenge," he said.
"She's called on the teaching profession to be involved in this challenge on getting our country back on its feet again. I think principals are certainly up for that, they understand that it's important that schools are open."
Rush said the next step for schools was figuring out how many students and how many teachers were going to turn up on Wednesday next week.
"We certainly do not want to see any vulnerable teachers back at the physical site, they need to be at home working remotely," he said.
The president of the Auckland Secondary Principals Association, Richard Dykes, said schools would not be able to provide much more than childcare during alert level 3.
"If a child does need to come to school, we will absolutely do that, we'll provide childcare and supervision, but it will be just that. Students will almost certainly be doing their online learning at school," he said.
"Potentially half our staff will be at home anyway because of their particular circumstances."
Dykes said principals had an important role to play in helping get the economy restarted again.
"I don't think there'll be a principal across the country who says I'm not prepared to do my bit," he said.
The president of the Secondary Principals Association, Deidre Shea, said the starting point for reopening schools would be the measures required to protect students' and teachers' health during the two weeks of level 3.
"All the peak bodies, including SPANZ of course, have been working closely with the ministry to get out some really clear guidelines and rules I suppose around some of the basic health stuff so schools are in a position to open safely," she said.
"That's got to give us the basis from which we can operate. Once we know that, we can make more nuanced decisions about the teaching and learning."
The government said people would be allowed into schools and early learning centres from today for cleaning and other preparations ahead of a teacher-only day on 28 April.
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