The Jodhpur-based varsity has also ordered an internal inquiry into the matter.
Menon, a Political Science professor at JNU, was invited to the seminar organised by the Department of English of Jai Narain Vyas University yesterday.
"We have filed a complaint with police against Menon and the organising secretary of the seminar, Assistant Professor Raj Shree Ranawat. We have also set up an inquiry team which will look into the entire episode," said Jai Narain Vyas University vice chancellor R P Singh.
It is alleged that Menon showed disrespect to the national flag and national anthem.