Assessment for those students could have a lifelong impact, he said.
It happened that those students were also able to be vaccinated, he said. "My message to them now is go out and be vaccinated if you haven't been - it will make returning to school all the safer when we're in a position to be able to do that."
Primary schools presented a much more difficult situation, as when they reopened they would become the highest concentration of unvaccinated people in New Zealand.
Daily Covid-19 case numbers were on a growth curve, and if the virus were to spread within highly concentrated pockets of unvaccinated people, that curve could get steeper.
"We're very very mindful of that when we are thinking about primary school settings."
While he would not set a date for when young children could return, Hipkins wanted them back "as soon as we can". It would be good for the kids and often their parents - but he was aware a lot of parents were anxious about exposing their children to Covid-19.
At this stage there were no plans to take different suburbs' vaccination rates into account when reopening schools, Hipkins said.
Auckland paediatrician Dr Jin Russell has called for a "gold standard" for Auckland schools when they reopen, including providing air filters as is being done in Victoria.
But Hipkins said he wanted to keep expectations realistic about air ventilation. He said there were more than 35,000 classrooms across New Zealand, and to install HEPA filters in every one would also require installing new air conditioning systems in many of them.
That could cost hundreds of millions of dollars, with the public health risk assessment showing in some cases keeping doors and windows open would work better, he said.
He expected more face mask use in educational settings, at least in the short term.
The Government was also considering options like rostering to avoid having all students on site at the same time. They had to ensure it was practical and would allow for teaching and learning.
Last Monday it was announced that people in an education setting who are in contact with children would have to have their first dose of the vaccine by November 15, and their second by January 1.
Healthcare workers would need to be vaccinated even sooner.
But nine days later the public health order that would make that mandate legally binding has not yet been signed off.
NZ Principals' Federation president Perry Rush told the Herald today the finer details of the mandate were still unclear - including whether teachers who had not been vaccinated by November 15 would have a job after that date.
Hipkins said it took time for the Government's instructions to be turned into legally binding documents.
"One of the constraints is just that getting it down onto paper is taking a little while."
There were also technical issues around who was captured by the mandate - for example, whether a sports coach, using a school field outside school hours, would need to be double dosed.
"We're working through the cases at the margin to make sure we're absolutely clear about who's in and who's out."
He was "ready and waiting with the pen" to read and sign the orders on the day he received them.
It was possible more legislative changes could be made around vaccination - such as changing law around the vaccination certificate.
Hipkins will be making further announcements about school reopening tomorrow.
