Protesters of the Trinamool Congress Employees' Union showed black flags to Dhankhar, who is the chancellor of the varsity, and blocked his car at gate number 5 of the campus at 10.30 am on Tuesday.
The protestors raised "go back" slogans and showed placards that read "No NRC, No CAA".
He left the premises at around noon.
Dhankhar said the incident showed that rule of law has been "severely compromised" in the varsity.
".@MamataOfficial. Am surprised that inspite of my directive to VC to go by rule book and abide by my direction as regards Convocation, the same has been started. In utter helplessness as of now I am leaving the Jadavpur University campus. Those concerned must soul search.
"@MamataOfficial. Events that have unfolded as a result of politically motivated orchestration of obstruction of my entry to JU to preside over the Convocation so that students get fruits of their labour, leaves no manner of doubt that rule of law is severely compromised," he tweeted.
The governor, in a series of tweets, hit out at the vice-chancellor Suranjan Das, saying he remained "silent spectator" to the incident.
#WATCH: West Bengal Governor Jagdeep Dhankhar at Jadavpur University after being blocked outside by protesting students, says"It's a painful moment for me as a Chancellor&Governor.There's total collapse of rule of law in the state.The state Govt has put education in captivity." pic.twitter.com/GcayRcxqef— ANI (@ANI) December 24, 2019
"I am amazed that the Vice Chancellor is in passive mode and silent spectator to this unseemly spectacle that augurs painful sliding of our system. This action is orchestrated by the powers that be not knowing the damage it causes in short and long run on out education.
"Neither the VC nor anyone else from the University has contacted me though I have from my side contacted them," he tweeted.
In another tweet, the governor said,"A painful scenario that the Jadavpur University Vice Chancellor is oblivious deliberately of his obligations and looking for alibis. He is presiding total collapse of rule of law. Ruinous state of affairs."
Meanwhile, Arts Faculty Students' Union president Debraj Debnath said that the students did not block the entry of the governor into the campus.
"We only showed placards and raised slogans against NRC and CAA," he said.
The governor was on Monday heckled and shown black flags twice at the university, a hotbed of anti-CAA protests, a day after he declared as "illegal and invalid" the varsity's decision to defer the December 24 special convocation because of possible trouble.
He had arrived at the varsity on Monday to attend a meeting of the university Court, its highest decision-making body.
After he could not attend the Court meeting due to agitation by stakeholders, including students and non-teaching staff, the chancellor had called up the vice-chancellor Suranjan Das requesting him to hold the meeting at Raj Bhavan.
But, the Court members unanimously decided that the meeting should not be shifted elsewhere as it had already started at the JU campus.