Teaching leaders warned schools would be forced to make cuts, increase class sizes and be prevented from expanding the courses on offer because of uncertainty surrounding a new funding system for post-16 pupils.

More than 100 secondary schools in Yorkshire have been denied extra money which they claim they need to cope with expanding sixth forms in the next academic year, the Yorkshire Post can reveal.

Instead these schools will be forced to cover the costs of educating 2,102 sixth-formers from their own budgets. The average funding for an A-level student is £2,945 a year, meaning Yorkshire schools would need around an extra £6.1m to plug the gap.

The chaos follows a new funding system introduced by the Learning and Skills Council (LSC) this year.

Across Yorkshire 126 secondary schools have asked for increased funding but just 20 are set to receive it, with the LSC claiming the increase in pupil numbers has placed pressure on its budget. The region's schools have predicted a 2,500 increase in sixth-formers from September.

The LSC, which funds post-16 education, has asked schools how many pupils they expect to have in their sixth forms next year. In the past the LSC has funded schools based on their previous year's student numbers and then made adjustments afterwards if schools had seen an increase or a decrease in sixth-formers.

The new system, which aims bring schools in line with colleges, is meant to fund schools based on their actual numbers – but schools predict a national increase of 28,000 sixth-formers – four times the rise seen last year.

Malcolm Trobe, the immediate past president of the Association of School and College Leaders, said the Government had failed to provide enough money to meet increased demand for places.

But he also criticised the new funding system for creating uncertainty over whether schools had genuine cases for asking for extra money.

Mr Trobe said: "The LSC has managed to get some more money from the Government but the grant is still not enough to meet the demand from people to stay in school after 16.

"But there has been a significant over-estimation from schools over their numbers. In some cases schools will have put their numbers together accurately but the system has not been rigorous enough in detecting which schools are accurate and which schools are 'over- egging' the pudding."

Headteachers across the region said the funding shortfall meant they would have to find money from elsewhere in their budget to cover the cost of their increasing sixth forms.

Chris Myers, the head of sixth form at Driffield School, told the Yorkshire Post his school had 40 students who would not be funded by the LSC.

He added: "Unfortunately there are limited funds and this has meant we will not be able to get an increase although we expect our sixth form to increase from 300 to 340 students. Hopefully we will be able to get the increase next year.

"It is a considerable increase and the lack of funding will mean we have to run larger classes of 25 students rather than 15 to 20."

Tom Ashworth, headteacher at Ermysted Grammar School, in Skipton, said his school was facing a funding shortage of between £45,000 and £90,000 from September.

He warned that the school would not be able to cope with similar shortages in future years.

Ken Cornforth, the head teacher at Pudsey Grangefield School and chairman of the Secondary School Headteachers Association in Leeds, said the lack of increased funding would hit new courses.

A spokesman for the LSC said it was impossible to work out how large the gap in funding was as different courses attracted different levels of funding.

He said: "From our perspective, we have two prime considerations when assessing their estimates. Firstly the potential for real growth in this area – the actual cohort numbers will necessarily govern and restrict any realistic assessment of growth and secondly we are managing a finite pot of public funding."

A spokeswoman for the Department for Children, Schools and Families said: "It is for the LSC to agree funding with each institution and the Government fund the demand if it can be delivered. The package announced on November 16, 2007, will see year on year increases for school sixth form funding with a four per cent increase in funding from 2007/08 at £2bn to 2010/11 at £2.1bn."