The government is giving schools extra money for relief teachers as it asks staff and students with cold symptoms to stay away from classrooms, it says.
About a million children and teachers are set to return to school after more than seven weeks away.
"Basically the presumption between level 3 and level 2 reverses. At level 3 we were saying keep your kids at home unless you've got a good reason to send them to school. When we move to level 2, that reverses: send your kids to school unless there's a good reason to keep them at home."
Those reasons include children being sick or having health conditions that put them at higher risk.
Hipkins said the government did not want to take a hard line against parents who were anxious about sending their children back to school.
He said he expected schools to be flexible as parents rebuild their confidence in their children attending school.
"We do want to see kids back at school and it's a real challenge for schools if they have to try balance dual learning."
Hipkins said students doing NCEA had been well informed by schools and NZQA had been supplying guidance to make sure kids were up to date.
"We are looking very closely at what the overall impact of it is and I'm awaiting some further advice from NZQA on some pragmatic changes that might be able to be made around NCEA timetables and things like that so that kids aren't unduly disadvantaged."
He said changes were made to assessments in the wake of the Christchurch earthquakes and he was now seeking guidance on whether a similar thing could be done on a wider scale.