Academics at the University of Hull raised concerns about an MA programme in security studies on which seven high-ranking Indonesian army officials were studying last year.
Student campaigners also protested, claiming that the presence of men linked to Kopassus, the Indonesian army's special forces, could stop other Indonesian students talking freely about events in their country.
The university said the course was recognised by the Economic and Social Research Council as one of the best in the country and people were recruited to it in the normal way.
A university spokesman said: "We don't select students or admit them to our courses on the basis of the politics of their home governments. If universities went down that road it would be very difficult to know where that would end."
Demand was insufficient to run the course this year.