The president of the Principals' Federation, Perry Rush, said he had been told of four cases of families deciding to keep their children home.
He said children should go to school and people should not panic one another.
"The virus is being successfully managed at the moment. It's not being spread person-to-person and I would just encourage parents to be thinking carefully about the importance of continuing to see their child go to school. Attendance every day that a school is open is really vital," he said.
"I think it underlines the importance ... of taking a really sensible and measured and carefully-considered approach to what is happening so we're not panicking each other into over-reacting."
Rush said principals were frustrated and children should be going to school while they could because it was possible that schools could be closed later in the year to stop the spread of the virus.
In Auckland, the president of the city's Secondary School Principals' Association, Richard Dykes, said he was aware of two cases of parents refusing to send their children to school.
He said the families were asking for online teaching of their children and it was not clear how schools should react.
"This is where we would like some guidance from the ministry because we're getting into legal issues," he said.
The principal of Wellington High School, Dominic Killalea, yesterday told parents it would support children's learning if they decided to keep them home.
"If you are apprehensive about sending your student to school we feel we are in a position to support your student's learning from home and this is no different from any normal student absence," he wrote.
Killalea told RNZ no families were keeping their children home from school, but he expected some might in future.
"We want people to just send kids to school as normal, but I'm also aware that some parents might be feeling a little apprehensive about that, and so if they are we're just trying to reassure them that we can support them if they are at home and that we treat that like a normal student absence."
The chief executive of the Early Childhood Council, Peter Reynolds, said in the past week several early childhood centres had reported that families were refusing to send their children.
"Parents have said 'look if you've got Asian kids coming into your centre what steps are you taking to protect our child against Covid-19', the implication being that for some reason it's tied to particular ethnic groups which of course we know is ridiculous. But also they're worried and they're saying 'we're going to withdraw our children for a period and keep them home'."
Reynolds said he could understand that fear and anxiety was driving the reaction, but it appeared that young children were less likely to be affected by the virus than adults.
The Education Ministry was calling every school in the country yesterday and today to check if they could teach students online in the event of a school closure.
Principals said they were not expecting a blanket shut-down of schools in the short-term, and it was more likely that schools would respond individually if cases of Covid-19 emerged in their community.
But the ministry's deputy secretary, Katrina Casey, said at this time there was no reason why children and young people should not be in education, nor for closing all the schools in the country.
"The scenarios that we're planning for are if we do need to close a school if there is a case in a school, or in a community that the school is very close to, and in that situation we're doing a stocktake to see what additional information we would need to put in place to help schools and parents out."
Casey said that included finding out what the barriers to online learning are, how many children do not have devices at home, now many families do not have access to WiFi, whether there are data caps that would cause an issue and what kind of telecommunications support would be needed.
She said that will allow them to start to have discussions with various telcos about what might be needed.
The most likely scenario for a school closure would be if a case occurred within a school, Casey said.
"And we need to shut the school initially for one to two days so the health authorities can trace and contact any close contacts and then evaluate the situation after that."