However, some in the region dispute the statistics.
The figures, obtained by Labour education spokesman Chris Hipkins, reveal 62 Otago schools (42%) posted net operating deficits in 2014, of amounts ranging from $1503 to $229,977.
Nationwide, 994 schools (40%) posted deficits in 2014.
Mr Hipkins said many of the deficits were higher than $100,000.
‘‘It is a shocking state of affairs that so many schools are running at a loss.
‘‘You would expect schools to be hopefully breaking even. Obviously, I don't expect them to be running at a profit, because they should be spending the money that they've been allocated for educational purposes.
‘‘But the fact that they're running at a deficit, and that so many schools around the country are running at a deficit, is concerning.''
His greatest concern was pupils may be missing out on things such as outdoor programmes, library books and technology.
Waitaki Boys' High School rector Clive Rennie was also concerned about the lack of Government funding for schools.
His school recorded a deficit of $229,977 in 2014, and while much of it concerned building projects, it showed the increasing cost of education, he said.
‘‘The importance of technology in the curriculum, particularly with computing, means schools are really struggling to find enough money to be right up to date with what they are offering kids.''
He said another contributing factor was the cost of getting people to help pupils with reading and writing difficulties had grown.
‘‘And if you're in a school where your literacy is a real issue and you've got a lot of those kids, then it's an expense that has grown and has never been recognised by the ministry.
‘‘So we're getting a few of those sorts of things where, definitely, the funding is not keeping up with the increase in costs.''
Mr Rennie said a major issue in the finances of Waitaki Boys' High School had been the cost of the ministry's intervention.
Commissioner Nicola Hornsey has been running the school since its board of trustees stood down in October 2014 over an employment issue.
‘‘At the end of 2015 we posted a deficit of around $76,000, and that amount equals what the school had to pay for the ministry's commissioner.
‘‘For the 2015 year, we would have had a surplus if we didn't have the intervention.
‘‘I can tell you, the cost of the intervention has not been kind to the school over the last two accounting periods.''
Green Island School principal Steve Hayward said he would also like to see more funding for teacher aides and education programmes.
However, he was surprised to see his school on the list with a deficit of $67,526, and he disputed the figures.
‘‘We've got money in the bank. It's just not true.
He said Green Island School carried out major property development works in 2014, and all of the money had been repaid.
He said the problem in many cases, was schools had to pay contractors' bills, but ministry funding for the project was drip-fed to schools.
If the school was not reimbursed before the end of the financial year, it would show up as a deficit, despite there being money to cover the amount, he said.
‘‘The figures don't show the entire picture.
‘‘I can show you our audited accounts that show our school has made a small profit every financial year.''
Mr Hayward said the schools that were genuinely in financial deficit, had ministry interventions such as commissioners, limited statutory managers or financial advisers.
At present, only East Otago High School has a ministry intervention to help the school's board of trustees control financial and property management issues.
A spokesman for the school said it was now back on track.
Ministry sector enablement and support head Katrina Casey said most schools were doing a good job when it came to managing finances.
She said the figures quoted came from the annual account records as at December 31, and were a snapshot of school finances on that date.
‘‘This is important, as schools receive their next instalment of operations grant [funding] on January 1 each year.
‘‘So reporting a deficit at a given point in time does not always relate to insufficient funding for the year.''
She said some schools recorded operating deficits because their rolls had decreased but the school had not amended its operating costs to allow for the decrease in pupil numbers.
Costs such as teacher salaries, are based on the number of pupils at a school.
‘‘It could also be in deficit because even though its expenses have not increased, its income was lower than expected for the year.''
She said reporting a deficit did not suggest a school was at risk.
‘‘Some schools report deficits whilst carrying adequate cash reserves to meet that planned deficit.''
However, if the ministry noticed persistent problems with a school's finances, statutory intervention could be used to help it return to financial health, she said.
