Nearly half of all schools with sixth-forms in England have reported errors in the pupil data being used to determine their funding for the next academic year.
Mistakes on the number of pupils successfully completing courses have the potential to leave large holes in secondaries' 16-19 budgets.
The latest errors were uncovered when the Young People's Learning Agency (YPLA) sent "success rate" figures back to schools to check.
A YPLA spokesman said "just over 900" or 48 per cent of schools had identified errors in the 200809 data which will determine post-16 funding levels from August.
Heads' leaders believe shortcomings in school computer software systems may have contributed to the problem.
Association of School and College Leaders policy director Malcolm Trobe said previous audits of school post-16 pupil numbers had revealed they were out by as much as 10 per cent.
Sixth-form funding used to be based on a national average course completion or success rate. But for 201112, schools are moving over to a system similar to that already used for FE colleges, which bases funding on institutions' individual success rates.
Mr Trobe said if the mistakes were in line with previous errors, they could leave schools with six-figure shortfalls.
"This really matters," he said. "The accuracy of post-16 data is of critical importance because it links with funding and is, therefore, subject to audit. It is absolutely essential that schools get it right."
Some FE colleges have been accused of artificially boosting their success rates to improve funding. In November, the Skills Funding Agency threatened to ban some colleges from receiving money because they were profiting from incorrect figures "by accident or design".
But Mr Trobe does not think schools are "gaming" their figures in the same way. He said the data collection or management information systems (MIS) used by some had not allowed heads to check their success rates before submission.
"I don't think anybody is trying to cheat the system at all," he said. "But there are a number of points in the system where errors can creep in.
"Sometimes this is human error in terms of data entry and sometimes it is because the MIS needed to be better.
"It is not that the schools or YPLA or the Department for Education are deliberately making errors. It is just that the checking at the start of the process is not very good."
The YPLA spokesman said: "This was the first time a checking exercise had been carried out for this data and we were pleased that a large number of schools responded.
"These schools identified some errors in the data and we were pleased the exercise allowed them the opportunity to correct any inaccuracies - which was the whole point of doing it."