Delays by the Student Loans Company in sending out data could hold up millions of pounds of funding for universities.
The SLC was due to send out statistics on the split of tuition fees between student and public contributions last month. Universities had a deadline of December 20 to certify that the students were in attendance at the beginning of the month.
Institutions expected the data to be dispatched by November 23, but some did not receive it until December 4. Now they will struggle to return the forms by the deadline.
Universities that cannot respond on time risk delays in receiving their fee payments, which are supposed to arrive in early February.
Roger Clark, academic registrar at Reading University and a member of a Department for Education and Skills student loans consultative group, said the problems were down to a misunderstanding between the SLC and the DFES. He had asked the DFES whether a deadline extension was possible.
"To what extent we can get an attendance return back to the SLC on time will depend on how much resource we can mobilise. Some universities will be able to do it and some won't," he said.
"Whether they get paid on time will depend on how fast the SLC can process the returns and how much slack they have built in."
He said the fees due in February would add up to millions of pounds for each institution. He estimated that for Reading they would be more than £2 million.
The SLC said: "Recognising the slight delay in dispatching the material, the SLC will guarantee to process any which do arrive a few days later than originally asked. Clearly there will be some flexibility in this, however, it will not apply to returns made more than a few days outside the targeted times.
"We can assure all HEIs that, should any deadline be missed for whatever reason, fee payments will still be made as soon as possible."