Calling the incident as "unfortunate", the minister said, "Kashmiris are citizens of India and part of our family. They should not be harassed."
The minister has also asked the home ministry officials to issue an advisory in this regard.
Six Kashmiri students studying at Mewar University were beaten up by some locals in Chittorgarh district.
In another occurrence, banners calling for boycott of Kashmiris and asking them to leave Uttar Pradesh came up in Meerut in the wake of rising incidents of stone throwing on security forces in Kashmir.
The minister said proper inquiry should be initiated in each case and strongest possible action should be taken against the guilty in both the states.
Mr Jani claimed they have put up these banners and hoardings along the Partapur bypass outside the colleges where Kashmiri students study.
The outfit had warned of a full-blown "Halla Bol" campaign from April 30 to "banish" Kashmiris who do not leave the state on their own.
Partapur Station House Officer Dinesh Sharma said the banners have been taken down and an FIR has been registered against accused persons for "promoting or attempting to promote disharmony on the grounds of religion, race, place of birth, residence, language, caste or community".
(With inputs from agencies)