The school budget deficits ranged from single digits to seven digits.

Almost 1000 New Zealand schools spent more than their income during a recent financial year.

In 2014, 994 schools recorded a net operating deficit, according to information released to the Labour Party.

Twelve schools, not identified in the information, owed more than they had in assets in 2014.

FAIRFAX NZ A budget deficit for a year is unlikely to cause ongoing financial issues in most cases, Education Minister Hekia Parata said.

But the Education Minister Hekia Parata said school finances aren't out of control if there is a net operating deficit in one year.

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Of the schools that spent more than they received in a financial year, deficits ranged from single digits to seven digits.

SIMON EDWARDS/FAIRFAX NZ The education system is under financial strain, Labour Party education spokesman Chris Hipkins said.

For example, the information said Christchurch Girls' High School recorded a deficit of $1.04m in 2014 - although the school refuted the figure saying it ended with a surplus - and Papamoa College in the Bay of Plenty recorded a deficit of $423,750.

Others were far smaller, such as $606 for Paeroa's Goldfields School and $241 at TKKM o Tapere-Nui-A-Whatonga in Gisborne.

Deficits showed the education system is under financial strain, Labour's education spokesman Chris Hipkins said.

FAIRFAX NZ Property work at Tai Wananga-Tu Toa in Palmerston North was the main reason for a 2014 deficit, tumuaki Toby Westrupp said. He's pictured, centre, with some of the students in 2014.

"I don't expect the schools to be making huge profits, but nor do I expect them to be going backwards."

Government funding hasn't kept up with schools' need for technology, he said, and schools are also dipping into operational funding to support students with special needs.

Parata disagreed.

"It is a bit like having a mortgage," she said. "In most cases this is unlikely to cause any ongoing financial issues. When schools do get into financial difficulty, assistance is provided."

Auditors told schools off if they had a budget deficit for a year, New Zealand Principals' Federation president Iain Taylor said.

"It's not good to budget for a deficit and the auditors don't like it, but if you have money invested in other accounts, it actually is not the end of the world."

Between 55 and 60 per cent of all schools operated in surplus in each of the last three years, the Ministry of Education said.

And the figures on deficits at individual schools came from a "snapshot" of their finances as at December 31, spokeswoman Katrina Casey said.

"Reporting a deficit at a given point in time does not always relate to insufficient funding for the year."

Some schools had cash reserves to cover their deficit, or it could be factored into a strategic plan.

Christchurch Girls' High School actually ended with an operating surplus of more than $200,000 for the 2014 year, board chair Michael Lay said.

He was unsure where the figures about a net operating deficit of $1.04m came from.

"We would be worried if we were running that sort of a loss," he said.

Timing of earthquake repairs on the boarding house and corresponding insurance payments could have affected how the books looked at certain points.

The school had managed a surplus but had to be enterprising to make sure it did, he said.

It had money in investment accounts and income from international students, community donations and its boarding house.

Tai Wananga, which has a campus in Ruakura, Hamilton, and another in Palmerston North, posted a deficit of $347,107 in 2014.

Property work on the Aokautere Palmerston North site was the main reason for that, tumuaki (principal) Toby Westrupp said in an emailed statement.

"Financial data and accounts information received to date suggest we will return a pre-audit surplus in 2015," he said.

At Tauhara College in Taupo, the 2014 deficit was $182,297.

Principal Keith Buntting, who has been at the school less than six months, said the school was working closely with the ministry and a specialist accounting company.

"A priority for us going forward is to minimise further deficits and, without reducing the educational opportunities for current students, slowly build up the reserves to buffer any future challenges."