Nearly one-third of all agricultural colleges have shut, and lecturers' union NATFHE predicted that normal teaching would not resume in most agricultural colleges until at least the autumn.
Many students would be unable to complete their qualifications on schedule because of the closures. Without extra cash some colleges may make some of their teaching staff redundant.
They have asked David Blunkett, the Education Secretary, to set up a task force to look at measures such as waiving work-based assessments for some qualifications, and supporting distance learning for those kept away from their colleges.
At Newton Rigg in Cumbria the first outbreak at a college has occurred. Cattle at a dairy farm showed signs of lameness, the vet was called, and the disease was confirmed the following day.
The farm and college were shut down and 450 cattle and 600 sheep were destroyed.
"We are not sure what kind of mpact this is going to have," said Andy Harris, marketing manager. The college has 700 full-time and 3,000 part-time students and they are all now off the campus.
"At the time it was a shock and like the end of the world. It is a big disaster but eventually we will re-stock - there is no doubt about that."
Chris Dyke, NATFHE's agricultural representative, said the situation had taken a sudden downturn. "We are in for a very long-haul."
The training and enterprise councils, which are to be disbanded at the end of this month, are trying to tidy their books, and get all apprentices or trainees to finish their work. But the colleges are saying that they cannot see or assess the students.
"Kirklees Hall in Northumberland is reduced to one receptionist. She is the only person there. It sounds like a ghost town," Chris Dykes said.
The image of farming is deterring students from applying for courses and jobs, says a report by the Further Education Funding Council.
Agriculture in further education - see www.tesfefocus.co.uk