The Governor has also called a meeting of Vice-Chancellors of all Universities where he was ex-officio Chancellor on January 13 next year.
Drawing the state government's attention, Dhankhar said he was writing to Banerjee "that she cannot afford to be in non functional mode at such dangerous developments in the temples of education".
"She needs to engage in her role as executive head. The designed confrontation with the Chancellor is not at all in the interest of the education or State. As Governor, I request her to discuss the issue with me after being fully updated about the incidents and would greatly appreciate if she can make it convenient for this in the coming fortnight," he said.
Dhankhar ran into fresh protests at the JU campus earlier in the day as a section of the non-teaching staff affiliated to the ruling Trinamool Congress showed black flag and blocked his car railing against his comments supporting the new citizenship law.
After waiting at the gate number five for around 90 minutes amid continuous shouts of "go back", Dhankhar finally left the premises around noon instructing the Vice Chancellor not to start the convocation.
However, even while his car was stuck at the gate, the university authorities went ahead with the convocation, saying there were such precedences and referring to the new rules framed by the state government curtailing and limiting the Chancellor's powers.
On Monday too, a large number of JU students and staff had blocked Dhankhar's car and staged a black flag demonstration, besides raising "Go back" slogans against him when he arrived at the campus to attend the JU court meeting.
Even while waiting in his car, Dhankhar continued to tweet, saying "rule of law is severely compromised".
Interacting with the media on Tuesday evening, the Governor said: "A few unwholesome developments and unseemly spectacles in educational institutions has pained me.
"There has been an effort backed by the state to usurp the authority of the Chancellor and immobilise his functioning by non state actors in the front and state actors in the background. These are indicative of a massive sliding down of the education scenario in the state."
Dhankhar said formal programmes of five universities have been cancelled "without reference to me as Chancellor" while he had "no input" from the Education Department.
He called it "paralysis generated by the state to control the Universities".
Dhankhar said he was not being informed about programmes in universities and castigated the new rules which entails "the Chancellor, who happens to be the Governor, communicate with the Vice Chancellors only through the Principal Secretary, Higher Education".
Calling the cancellations "remote controlled", he said "the Universities are in political cage."
On the JU developments, Dhankhar regretted he could not attend the court meeting despite being in the campus for two hours.
Dhankhar said on Tuesday a "handful of people held the system hostage with all concerned in the State Government and University being in passive mode".
"Difficult to repel the thought that all this was being orchestrated with the support of the University and government."
He said after being on the campus for over an hour he returned as the Vice Chancellor had in "defiance" of his directive conducted the convocation.
"The strategy to compromise the position of Chancellor is unfortunate and counter productive," he said.
"To overcome this slide down and to contain this detrimental impact on the career of students", Dhankhar said he has called a meeting of all the Vice-Chancellors "for a thorough interaction" at Raj Bhavan on January 13.
( With inputs from IANS )