He also said the students are like "yuva bombs" and called upon the Centre to refrain from handling the students in this manner.
Thackeray's statement came after many students and staffers were injured during a protest at the Jamia University on Sunday and triggered protests in campuses around the country, besides echoing among Indian students studying in American universities.
In a quick retort, Leader of Opposition Devendra Fadnavis said that comparing the Jallianwala Bagh massacre with the Jamia University incident by the CM was "a big, big insult to all the martyrs who have sacrificed their life for our nation".
"Entire Maharashtra and India wants to know if Uddhavji agrees with these (Jamia students) slogans? By promoting and encouraging such agitations, it is now very clear to what extent Shiv Sena has stooped down on compromises for personal greed," said the former Chief Minister.
Dwelling on the Citizenship Amendment Act (CAA), Thackeray said there appears to be no clarity over how many people will enter the country and from where, and wondered where they would settle after coming here.
He pointed out that the BJP-led central government appears to have no idea where and how it will settle the Hindus and other immigrants who would get Indian citizenship after the CAA.
Speaking on the occasion, Sena MP Sanjay Raut announced that his party (Shiv Sena) will not be joining the delegation that plans to meet President R. N. Kovind on the CAA later on Tuesday, but the CM will decide about the implementation of the CAA in Maharashtra in the cabinet meeting.
The CAA aims to grant citizenship to Hindus, Sikhs, Buddhists, Jains, Parsis and Christ facing religious persecution in Afghanistan, Pakistan and Bangladesh and have taken refuge in India on or before December 31, 2014.
( With inputs from IANS )