A third of Council-run secondary schools in Yorkshire and the Humber are running at a loss, it has emerged.
Across England as a whole, the number of secondary schools in deficit has nearly trebled in four years, according to a study.
It suggests that just over one in four secondaries in England is in deficit.
The study, published by the Education Policy Institute (EPI), comes amid continuing concerns about a squeeze on budgets.
Ministers have insisted that more money is going into schools, although earlier this month Education Secretary Damian Hinds did acknowledge that funding is "tight".
The EPI study analysed the balance sheets and budgets of 1,136 secondary and 13,404 primary schools in England over seven years.
It concludes that the number of local council-run secondary schools in deficit dropped from 14.3% in 2010/11 to 8.8% in 2013/14.
But between 2013/14 and 2016/17, the numbers in deficit nearly trebled to 26.1%.
It notes that the region with the highest proportion of local authority secondary schools in deficit was the South West, at 34.9% in 2016/17, while the lowest was the East of England at 17.5%.
The figures also show that the proportion of council-run secondaries in deficit in the East Midlands in 2016/17 was 22%; in London it was 28.5%; the North East 26.7%; North West 25.1%; South East 22.8%; West Midlands 24.6%; and Yorkshire and the Humber 33%.
The figures only cover local authority schools, and not other state schools such as academies.
At primary school level, the proportion in deficit across England dropped from 4.4% in 2013/14 to 3.8% the following year (2014/15), before rising to 7.1% in 2016/17.
David Laws, EPI executive chairman and former Lib Dem schools minister, said: "This analysis highlights the nature and scale of cost pressures facing England's schools. After 15 years in which school funding has either been growing healthily or has at least been protected from inflationary pressures, school budgets are clearly now being squeezed.
"This is evident from the sharp rise in the number and proportion of local authority schools which are in budget deficit. The trebling of the proportion of maintained secondary schools over recent years is particularly striking.
"Many schools will need to find savings and it will not be easy to do this without reducing staff numbers. Schools and the Education Department will need to work hard to ensure that reduced staff numbers do not impact on education standards."
Geoff Barton, general secretary of the Association of School and College Leaders, said: "This report shows that many schools are so cash-strapped they are unable to afford even a meagre pay rise of 1% for their staff next year without having to make further cuts.
"The Government has failed to provide schools with funding for pay awards over the course of several years, and this is one of a series of additional cost pressures which have pushed school finances to breaking point. Staffing cuts are not just likely in the future, as the EPI report suggests, but have already taken place in many schools.
"If the Government values education, it must put its money where its mouth is and provide schools with the funding they need to give all of our young people the very best start in life, and it must fully fund decent pay awards for school staff after years of austerity."
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