Principals of the most flood-damaged schools say it will be many weeks before they reopen their classrooms.
Floods have damaged more than 370 schools this year and seven are so badly affected they are still closed.
In Hawke's Bay, Eskdale School's classrooms were above Cyclone Gabrielle's floodwaters, but its grounds were still under a thick layer of silt and its septic system was broken.
The school's principal, Tristan Cheer, said the school was determined to reopen elsewhere and on Wednesday it started classes in sports club buildings at the Petane Domain with senior students bussing to a school that has spare classrooms.
"It certainly was an enormous mission but one that's well worth it in seeing the children's faces come in this morning," he said.
Cheer said 94 of the school's 300 children were displaced and teachers knew it was important to get pupils back to class to help them recover from their experience.
"They're certainly happy to be back at school but you can tell, particularly with the parents dropping the kids off and with the children themselves for some of them, scratch beneath the surface and there's still a lot of worry and a lot of pain there that we'll have to work through," he said.
Cheer said he hoped the school could reopen at the start of term two in late April.
The principal of Omahu School near Hastings, Te Kewena White, said he was waiting for a report on the school's flood and sludge-damaged buildings, but he doubted the 124-year-old school would reopen before the end of the first term.
"The slush, it was thick, it's contaminated because of what's in the water and we lost all our stationery, we lost everything. But the neat thing was we were able to save a log book that dates back to 1899. So that's the state of the school. We can't be there," he said.
This week the school's 28 pupils relocated to the hall at Flaxmere's Irongate School where the welcoming pōwhiri included a particularly appropriate whakataukī.
"What was said in the speech was ko tō raurau, ko taku raurau ka ora te iwi, which means your basket and my basket, we are able to get through this. It was quite emotional that they received us, they received students who no longer have homes, they received students who are traumatised," White said.
The school's children were resilient and they now had a place where they could get into a school routine and share their feelings, he said
Cyclone Gabrielle hit schools in other regions too.
In Wairarapa, Tinui School principal Simon Couling said the school went under a metre of floodwater and had moved into nearby playgroup and council buildings while the damage was repaired.
"It's like moving a house. Boxes and boxes and boxes of things that we just had to shove in a box and move across. So we're trying to unpack, get our storage, get some things like basically our photocopier working, an office table for our secretary and just all that basic stuff is slowly coming."
The school had immense community and official support, but it had been exhausting, he said.
"We're getting there but it's quite frustrating. We're very tired and everything seems like a bit of a mountain but there's been amazing support from the community, from the ministry, from the council especially letting us use the buildings.
"So we've been very blessed in that way but still got a long, long way to go and you know running a school's tough enough, but running a school that's a sort of a mobile school is quite daunting," he said.
Couling said he hoped the school could reopen in six months.
Tinui was on a list of flood-prone schools even before Cyclone Gabrielle and Couling said he was unsure if its buildings would be raised higher or the school moved.