Just 50 colleges had returned final claims, estimated to run into hundreds of thousands of pounds, to the Further Education Funding Council by last week as instructed.
Hundreds of others were still grappling with flawed computer software used to calculate funding.
The FEFC is trying to iron out problems which have left some colleges thousands of pounds adrift after calculating the amount of cash they can claim for teaching.
Concern is mounting among many managers and auditors over continuing problems with the Individualised Student Record - the detailed statistical return made by colleges to the FEFC. The records are the basis for funding claims.
Major audit firms including KPMG and Coopers Lybrand are warning colleges their ISRs do not stand scrutiny.
An insider at one leading firm admitted: "We had not signed off any ISRs by the deadline. Colleges are doing what they can, but some are really shrieking. There is a lot of discontent."
The latest broken deadline comes less than three months after the FEFC was forced to push back the college annual account deadline - also delayed because of struggles with the ISR.
The FEFC has maintained that colleges are responding well to the tough challenge of the ISR system.
Several principals plan to raise their concerns at the FEFC's annual conference today. They will complain that they still do not know exactly what cash they will receive for the previous academic year.
Among the latest headaches for finance managers is a problem with the software commissioned by the FEFC to allow colleges to calculate their final funding unit claims for the academic year 1994-95.
The programme should permit colleges to match up student data submitted at the end of that year - last August - with a final version including information on exam results. However, software problems mean colleges are having severe difficulties reconciling the two sets of figures, causing their funding claims to appear as much as 10 per cent out.
A mismatch can result in the FEFC clawing back cash, even though colleges may have earned it.
Managers are left to adjust their claim manually, to the fury of many. One principal said: "The software is effectively a black box - we have no idea how it reaches the figures it does. All we know is they bear no relation to the real numbers, and we are left virtually counting the heads of tens of thousands of students."
Adrian Perry, principal of Lambeth College, south London, said the software had vastly over-calculated the amount of funding units his college was owed for 1994-5. He said: "One of the most awful things is the constant denial from FEFC officers that there is any problem."
At nearby Lewisham College, principal Ruth Silver has written to FEFC finance director Roger McClure suggesting the FEFC's desire for detail and accuracy in recording exam results ends up defeating its desire for promptness in funding claims, and calling for longer deadlines next year.
Julian Gravatt, senior registrar at Lewisham College, said the FEFC had not learnt the lessons of pilot tests in which colleges had failed to submit returns on time.
He said: "If there is absolutely no change in the funding methodology or the political scene for the next three years, I am sure the system will eventually work. But given that there is an election round the corner some change is inevitable."
The FEFC has not officially extended its February 5 deadline, though auditors have written to colleges independently to reschedule their own visits and allow extra time.