The governor, who is the chancellor of the university, too faced demonstrations by the students belonging to SFI, Left leaning AFSU and FETSU and AISA, a naxalite sudents wing and a few members of the TMCP, university sources said.
They blocked his way and thumped the bonnet of his vehicle as the policemen kept requesting them to withdraw whicle the governor was seen helping Babul Supriyo to the vehicle.
Dhankhar and Babul Supriyo finally left the campus late in the evening hours after university teachers stepped in and persuaded the agitating students to lift their blockade, a spokesman of Jadavpur University Teachers Association (JUTA) said.
Meanwhile, stick-wielding supporters of ABVP, who had held a seminar in the campus during the day which sparked off the unrest at the university, vandalised the room of the Arts Faculty Students Union (AFSU).
Shouting 'Jai Shree Ram' and 'Bharat Mata ki Jai', the ABVP supporters were seen setting fire to furniture, computers and ceiling fans of the room and covering the signage outside it with black colour. They even painted ABVP on the wall of the room and burnt tyres before gate number four of JU.
The governor left in his vehicle through gate number three, university sources said.
The trouble began when Babul Supriyo, the union minister for environment, forest and climate change went to JU at around 2.30 pm to address the seminar by ABVP, the students wing of the RSS, at an auditorium inside the campus.
The union minister who was accompanied by Agnimitra Paul, a BJP leader, was initially stopped from entering and was left waiting just inside the gate for around one-and-half hours by the Left students unions, who raised slogans 'Babul Supriyo Go Back' and waved black flags at him, varsity sources said.
AFSU leader Debraj Debnath, who participated in the protest, asserted that "fascist forces" will not be allowed in the campus.
"We will not let BJP, RSS or ABVP to spread their ideology in a liberal institute like JU," he said and maintained that Babul Supriyo had misbehaved wth the agitating students, many of whom were women.
Babul Supriyo told reporters that the TMC government in the state will be held responsible for any eventuality.
"I did not come here to do politics. But I am saddened at the absolutely deplorable behaviour of some of the students of the university - the way they have heckled me ... They pulled my hair and also pushed me," Supriyo, who attended the seminar amid heavy security, said.
He also claimed that the protesters tried to provoke him by "openly referring to themselves as naxals".
As he prepared to leave after attending the seminar, he faced demonstration by the students again and was stopped.
At one point, he was seen sitting on the bonnet of his car and arguing with the agitating students and gesturing at them as they booed at him. He said he was not intimidated by their actions.
Dhankar said that the "gherao" of the union minister by the students is a very "serious matter" and asked the state chief secretary to take immediate action in the matter.
"The incident is an adverse reflection on the law and force agency in the state," Dhankhar told PTI.
According to the university sources, JU Vice- chancellor Suranjan Das fell sick during the agitation and was rushed to a nearby hospital.
JUTA spokesman said it is a 'black day' in the history of the 64-year-old university.
Any individual has the democratic right to come and participate in a discussion in the university irrespective of his ideology but the entry of police inside the campus and vandalising of students union rooms by outsiders cannot be condoned.
BJP national general secretary and the party's Bengal minder Kailash Vijayvergiya said the incident is an ample evidence of worsening law and order situation in Bengal.
"In a state where a union minister and Governor is not safe, you can very well understand the condition of common people. The TMC government and the police allowed this to happen," he said.
Extending support to the union minister, BJP Rajya Sabha MP Swapan Dasgupta in a tweet criticised the agitators for creating a "disgraceful scene".
"Disgraceful scenes in Jadavpur University as pro- naxal students supporting azadi in Kashmir block entry of @SuPriyoBabul. All this happening despite attempt by VC to appeal for calm. This is the state of some of our universities where a small minority flex their muscles," Dasgupta posted on the micro-blogging site.
Union Petroleum Minister Dharmendra Pradhan blamed the Trinamool Congress (TMC) and the Left for the incident.
He tweeted: "Shocked and appalled to see the way Union Minister Babul Supriyo was manhandled in Jadavpur University. Strongly condemn this extreme left hooliganism by Didi's goons. Bengal has become a breeding ground for lawlessness & anarchy under Mamata Banerjee. Absolutely crass & inhuman!"
Tripura Chief Minister Biplab Deb, who uprooted the decades-old Left government of Manik Sarkar in Tripura, called it "hooliganism". He expressed shock at how Jadavpur University has allegedly turned into a "breeding ground for extreme Left hooliganism".
He tweeted: "That's why all over India people have rejected Left parties".
BJP spokesperson Shahnawaz Hussain pinned the blame squarely up on the Students Federation of India (SFI), a leftist union.
He tweeted: "Really anguished to see the state of affairs in West Bengal, where Union Minister Babul Supriyo ji was attacked by the SFI goons. These goons could have the audacity to attack a Union Minister only because they are backed by the state government."
The National Secretary of BJYM, BJP's youth wing Impreet Singh Bakshi blamed it on the "political hatred". He attached a photo where a perpetrator is seen pulling the hair of the Union Minister. He took a dig at the Bengal administration saying: "Kolkata -- a city of supposedly a democratic, free India".
On Friday, Jal Shakti Minister Gajendra Shekhawat also tweeted, slamming the Left and the Mamata government.
Karnataka BJP MLA Shobha Karandlaje highlighted the muted response from the "Entire tolerance & award wapsi brigades".
BJP MP from Darjeeling Raju Bista demanded stern action against the hecklers. He demanded, "All those responsible for this heinous assault will have to be brought to the book".
Union Minister Babul Supriyo faced stiff opposition from students of the Left student unions at Jadavpur University in Kolkata when he visited the campus on Thursday that resulted in violence. He later alleged that Chief Minister Mamata Banerjee tried to delay his rescue.
The student Debanjan Ballav's ailing mother Rupali had urged Supriyo home "with folded hands" to pardon his son as handing him over to the police would ruin his career.
"Dear auntie, don't worry. I will not take any action that will harm the career of your son," the minister said in a tweet on Saturday, and attached to it a newspaper clipping about the request of the woman who lives in Barddhaman town.
"I wish he learns from his mistake. Neither had I lodged any FIR against anybody, nor allowed anyone to do the same. Get well soon," Supriyo said in the micro-blogging site.
The newspaper clipping attached to the tweet carried a photograph of teary-eyed Rupali Ballav with her hands folded.
In a video, her son Debanjan was seen arguing angrily with the minister and pulling his hair at one point of time in the university campus and pulling his hair at one point.
The BJP MP from Asansol had on Thursday expressed outrage over "the behaviour" of the agitating students describing it "absolutely deplorable".
Ballav, a student of Sanskrit College and not of Jadavpur University, however, said, "I only wanted to convey to the minister my misgivings about NRC exercise which will render crores of people homeless. But the minister became agitated."
Supriyo came to the university to attend a programme of the ABVP.
The General Secretary of Arts Faculty Students' Union (AFSU) Debraj Debnath said he has no knowledge about anyone named Debanjan Ballav taking part in Thursday's agitation.
"Mainly the students of the Jadavpur University took part in the protest on Thursday against the entry of BJP leader Babul Supriyo into the campus, who is known to have made inflammatory statements in past," Debnath told PTI.
The protest rally on Friday "against the bid of fascist forces like ABVP to enter the campus" was attended by thousands of students from various colleges in the city to express their solidarity, he said.
The AFSU had on Friday alleged that 'outsiders' vandalised its union room and broke windowpanes of the Arts faculty building.
The AFSU could not explain why a student of Sanskrit College, affiliated to the Calcutta University, was present during an agitation at the JU.
A source in the Jadavpur University Teachers' Association (JUTA) said to his knowledge Thursday's agitation was mainly organised by AFSU, SFI and All India Students' Association (AISA) members of the institute.
However, some students from other colleges and universities also attended an AISA programme inside the campus earlier in the day and some of them might have joined the JU students during their protest against Supriyo, the source said.