Almost 1,000 local authority schools and more than 100 academy trusts in England are now in debt, ministers have revealed in an answer to a parliamentary question.
Heads and teachers have been complaining about deepening problems with funding shortages – with warnings they might have to cut school hours.
The ministerial response shows 5% of council schools have budget deficits.
Lib Dem leader Tim Farron said funding gaps had become a “national scandal”.
“Over 1,000 schools are in the red. This should be worrying to every parent,” said Mr Farron.
His party had asked ministers how many schools and academy trusts, which run chains of schools, were in debt.
There have been growing warnings from schools about problems with funding.
The heads of every state school in West Sussex recently sent a letter to Downing Street, warning that they would have to consider cutting school hours or making teachers redundant if they did not receive emergency funding.
They warned that schools faced a “dire financial position”.
In a debate this week on school funding in West Sussex, MPs backed their concerns.
Sir Nicholas Soames, Conservative MP for Mid-Sussex, said funding arrangements were “unsatisfactory and unfair” and budget shortages would have a “damaging effect” on schools.
Tim Loughton, Conservative MP for East Worthing, said there was “nothing left in the tank” for many schools and that head teachers were telling him that school finances were at “breaking point”.
Head teachers say that budgets have not kept up with rising costs.
There are also particular regional shortfalls, with the government postponing plans to introduce a national funding formula aimed at addressing local anomalies in funding levels.
Education Minister Nick Gibb’s reply to the question on schools in debt showed that in 2014-15 there were 113 academy trusts with a revenue deficit, representing 4% of trusts.
There were 944 local authority schools in deficit, representing 5.3% of such schools.
The National Association of Head Teachers said problems with school funding were “very serious”.
A spokesman said a survey showed that two-thirds of schools were “dipping into reserves to stave off deficits” – and there were fears that rising costs would make this worse.
“I worry that in order for schools to bring their budgets in line to repay their debt, they will have to look at cutting staff, which makes up for 80% of the school expenditure,” said Mr Farron.
“There will be less extracurricular activities, IT equipment or even books as cash is funnelled into clearing the debt.”
Kevin Courtney, general secretary of the National Union of Teachers, called on the government to provide “immediate additional funding”.
“School budgets are being cut to the bone, and many more could find themselves in debt as the funding crisis worsens.
“We estimate that 92% of schools in England could face real terms budget cuts over the next four years.”
But Department for Education spokeswoman said: “All academy trusts must balance their budget from each academic financial year to the next.
“We continue to monitor the tiny number of trusts which reported a deficit at the end of the academic year 2014-15.”