"Widerstand's" first issue is dedicated to student protests across India after suicide of Rohith Vemula.
A students' magazine launched last week in Puducherry has been forced to stop distribution after protests over its debut issue comparing the centre's education policy to "saffron concentration camps".
Lieutenant Governor Kiran Bedi reportedly asked the Pondicherry University for an explanation on the controversy around the "Widerstand" magazine.
On Thursday, Ms Bedi reportedly met the university's vice chancellor Anisa Khan and was briefed.
Around 4,000 copies of the magazine - 7,000 copies were published - are locked up on the orders of the university.
Activists of the BJP and the student body linked to it, the Akhil Bharatiya Vidyarthi Parishad (ABVP), want the magazine banned. They have been protesting since Wednesday.
"Widerstand's" debut issue compares the centre's education policy to "saffron concentration camps".
A group of students took out a rally yesterday after protesters burnt copies of the magazine.
"Widerstand's" first issue is dedicated to the student protests across India after the suicide of young researcher Rohith Vemula at the Hyderabad university in January. Mr Vemula, a Dalit, hanged himself days after he was banned from parts of the campus for allegedly attacking an ABVP activist.
The death of Mr Vemula is described in the magazine as "institutional murder".
"Concentration camps? Don't make this a place an indoctrination camp for your SFI (Students Federation of India) ideology," said Monika Sethuraman, a student who opposes the magazine.
Manish Mahapatra, an ABVP member, alleged: "They are creating communal tension in the name of caste and religion".
The magazine's editorial committee has defended its content. "The e-magazine was published with the approval of the faculty in-charge," said Anjali Ganga, the editor.
"Right wing groups are trying to curb dissent and freedom of expression. This is what happened in other universities and now it's happening to us," she added.
Nitin Lal, a student who supports the magazine, questioned: "Is criticizing the government a crime?"