In his letter to the minister, Zameer Uddin Shah said if "certain elements" go ahead with their plans to hold a demonstration at AMU on December 1, "it could lead to massive student unrest at the campus".
However, the VC did not take the name of any party or outfit.
The Vice Chancellor has pointed out the possibility of "communal conflagration if political machinations are not controlled".
Some BJP leaders have decided to hold a demonstration on the campus on the birth anniversary of Raja Mahendra Pratap, an alumnus of AMU, whose family was closely associated with Sir Syed Ahmad Khan, the founder of the institution.
"Some elements are threatening to hold a demonstration on the grounds that Raja Mahendra Pratap donated large tracts of land for establishment of AMU and should be honoured accordingly.
"We have always acknowledged that the Raja did lease 3.04 acres of land to AMU in 1929 at a rate of Rs. 2/- per annum. We are proud of this freedom fighter. However, there were a large number of other donors and the main campus of the AMU was built on a land procured from the British government originally belonging to the Aligarh cantonment," he said.
Some local and state BJP leaders had recently claimed that AMU was built on land donated by Raja Mahendra Pratap but AMU authorities "failed to acknowledge his contribution".
The Vice Chancellor said that in order to defuse the situation, they had agreed to hold a joint celebration on Raja's birth anniversary
"On November 25, at the instance of some ex-servicemen of this district, who offered to mediate, I held a meeting with representatives of some outfits who are threatening to hold the demonstration. The idea was to defuse the situation and we agreed to hold a joint celebration of the Raja's anniversary".
However, the decision to observe the anniversary has now been revoked due to reports that there are internal differences within the group which was holding the protest, he said.