Nearly 1000 schools posted a deficit in 2014 and Labour says they were under strain because of Government under-funding.
The Government says the situation is better than it was in 2007, when Labour was in power.
Labour's education spokesman Chris Hipkins released figures today showing that in 2014 there were 994 schools in deficit.
"Many of those deficits were higher than $100,000 and one school's was more than $1 million," he said.
"It's a shocking state of affairs that so many schools are running at a loss -- there have already been concerns this means students are missing out on outdoor programmes, library books and technology."
Education Minister Hekia Parata says 40 percent of schools were in deficit in 2014.
"The proportion is lower now than it was in 2007 when Labour was last in office," she said.
"Then, it was 44 percent."
Ms Parata said most schools managed their finances very well, and an operating deficit in a particular year wasn't unusual.
"That does not mean their finances are out of control," she said.
"When schools do get into financial difficulty, assistance is provided."