About 250,000 children were expected to return yesterday as Auckland moved to alert level 2.5. but many stayed away.
Principals say parents are more fearful following Auckland's second outbreak and they would rather not take the risk of sending their children back to school.
The rest of New Zealand is at alert level 2.
Hipkins told RNZ's Morning Report programme today he wouldn't be asking students to go back if he thought it would put them at risk.
"All of the new cases that we're seeing of Covid-19 in the Auckland community are coming from known contacts so these were people who were already isolating so they wouldn't be in school and they wouldn't be in the workplace.
"That should give people reassurance that this cluster is being contained and therefore our decision to move down to alert level 2 is a justified one."
Hipkins said cases where there was a connection with a school were identified some time ago, the students and those around them had been tested, and the incubation period had long passed.
"We wouldn't be asking schools to reopen if we thought that was going to place students at risk.
"There is no good reason not to be sending your kids back to school at the moment."
While schools can use masks, there was no plan to make them mandatory.
"One of the challenges with young people is that it's difficult to make sure that they keep them on and sometimes if you've got kids taking masks on and off the value of those masks quickly disappears and you potentially increase risk," Hipkins said.
"The current health advice is that in a school setting masks wouldn't necessarily increase protection and in fact could do the opposite."
