Damaged or not, all Auckland schools will have a delayed start to the first term of the year.

The Education Ministry's ordered all schools, kura, early childhood services and tertiary institutes to remain shut for on site learning until February 7.

Principals were told the instruction was issued after the National Emergency Management Agency (NEMA) asked the ministry to help minimise traffic on Auckland roads while vital infrastructure is repaired.

The order covers the area from Wellsford in the north to Pukekohe in the South.

Secondary Principals' Association President, Vaughan Couillault said he was surprised.

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"We weren’t expecting that to be fair, but the principals I've spoken to in the last 20 mins all sort of go, 'we understand'.

"It’s not about schools not being safe."

A number of schools that were hit by flooding were already planning to stay closed for at least a day, including Remuera Primary School.

Principal Stephen King said a storage room on their campus has been left in a particularly bad state, after water levels inside reached one metre.

On top of that he told 1News: "The hall has leaked quite badly, we've had a resource room that's leaked quite badly and then probably two or three other classrooms where it's obvious leaking's occurred.

"I'm sure there's things I've missed. We decided what was going to be safest for staff and students was to take a moment, pause, ensure the campus was fully safe for kids to return."

He said matters were complicated by staff facing the need to clean up their own homes, and others being stuck outside of Auckland.

But the school was only planning to delay the start of the term by one day. He, like other principals, is disappointed to be facing a messy start to term one.

"We were looking forward to an uninterrupted year of teaching and learning. The teachers had worked so hard over the summer to get ready for this year and welcome kids back and do regular school.

"That's the punch to the stomach that's a bit hard to swallow."

A number of other schools 1News spoke to, with flooding damage, were planning to open on time regardless.

Principal of St Mary's School in Northcote, Paul Coakley, earlier told 1News: "We have had some water get into a couple of classrooms, but will start as scheduled on Wednesday.

"We will accommodate the classes elsewhere in the school for the first few days."

Auckland Grammar School had flooding in 12 classrooms but after ripping up carpet was planning to open too.

Principal Tim O'Connor said: "We've had the pandemic, now the floods... we were all in absolute agreement that we won't go into hybrid learning we don't want people thinking its another pandemic.

"That's one of the reasons why it's so important for us to actually get operating."

St Leonard's Road School in West Auckland is already open, but not for class. It's a Civil Defence Community Centre.

Principal Sharon Fuemana said, due to that, it was already set to stay shut for students until Tuesday.

The Education Ministry said: "Principals and education leaders have done a fantastic job of readying their schools for opening, and I know that this decision will be upsetting for some of them and for some parents."

It said the decision from the Secretary for Education comes as NEMA prepares for further weather damage.

Schools and kura have been told they can open for onsite instruction but need to provide distance learning.

"Early Learning Services may allow the physical attendance of any child whose parent needs them to do so, in the same that we did for Covid, but must otherwise be closed," it said.

Couillault said schools are unlikely to launch online lessons.

"It’s pretty hard to turn on online and digital learning when classes haven’t started."

He called the order a "minor annoyance", saying it's nothing schools can't overcome.

A number of schools have been reluctant to follow the order from the ministry, mostly due to not receiving the memo personally.

At around 5pm on Monday, Auckland Grammar said it still hadn't heard directly from the ministry, and was intending to go ahead with term one as planned.

"If your personal circumstances are such that you cannot transport your son to school safely tomorrow, then he should stay home," it said in a memo to parents.

Macleans College in east Auckland initially said it'll push on too.

On its website, the college said: "The school buildings and grounds have come through the stormy weather largely unaffected."

It later issued an updated statement reading: "Tonight schools have been given a further update and clarification about opening for students. Despite an earlier indication that schools could be open that is no longer possible.

"We will be closed. Students are to remain at home."

A number of parents have raised concerns about the lack of notice and unclear communication.

A mother that contacted 1News said her school emailed parents at 5pm citing "reliable media sources", but it had not received a memo from the ministry.

She said, "While I understand the need for caution but surely this should not have been a blanket decision for all and to delay by a full week when maybe a day or so would suffice."