A police officer said the university authorities lodged an FIR without naming anyone alleging ransacking of institute's properties by some people in the New Town campus.
The officer said some students damaged glass panes in the compound while agitating before the Vice Chancellor's room.
A section of students alleged authorities did not listen to their long-standing demands for better infrastructure facilities and alloting grace marks to qualify for tests.
The Trinamool Congress Chhatro Parishad unit of the institution, which controls the students' union, denied any of its activist was involved in the ransack.
Aliah is a state government controlled minority autonomous university in West Bengal.