The South African Students Congress has accused the University of Limpopo (Turfloop campus) of a "political witch-hunt".
This follows last week's decision to expel 30 students, half of whom belong to the Pan Africanist Students Movement. The students' protest resulted in the destruction of R600000 worth of property.
Students protested against an alleged decision to increase fees from R4200 to R5000 next year.
Sasco Limpopo chairman Mpho Sebola said yesterday: "It is clear that management is waging an ugly war against some organisations and leaving others untouched."
Sebola said management did not target ANC youth league members.
University spokesman Kgalema Mohuba said students' expulsions were based on information from private investigators and the police.
"It is unfortunate that the list excluded ANC youth. Though students were allowed to write exams, internal disciplinary measures will take place."