In an editorial "Unmasking pseudo-Ambedkarites" in its lastest edition, RSS also attacked Rahul Gandhi for visiting Mhow on the birth anniversary of Ambedkar.
It said use of institutional space and symbols without permission amounts to "indiscipline" and the institution has every right to question students.
Organiser also said educational campuses are "afflicted with red ideology" and forums like Ambedkar Periyar Study Circle in IIT-Madras are used for "propagating anti-Hindu and anti-Bharat divisive ideology", which Ambedkar would never have approved.
"Nobody can and should support ban on any student outfit for criticising government policies; definitely not, if the students are talking about caste-based discrimination in education sector," the editorial said.
It said there is neither any ban from government nor the notice issued to APSC for criticising the prime minister, as propagated by the group and secular media/intellectuals, and the HRD Ministry had only forwarded a complaint by another section of students.
"The issue of administrative disciplinary action against the Ambedkar Periyar Study Circle in IIT-Madras and Rahul Gandhi turning to Ambedkar birth memorial are "similar attempts to mask great nationalist reformers like Babasaheb with Communist garb of class divisions or Congress' way of vote bank politics," the editorial said.
The mouthpiece also accused Congress of "always misusing national icons" and attacked Rahul Gandhi saying, "appropriating anti-Brahminism movement was part of that strategy. No Indian would believe that a person who took ten years to understand his party will rightly address the complex issue of caste-based discrimination and untouchability."
The RSS mouthpiece said that "pet projects of Aryan invasion, inciting hatred, breaking democratic norms of discourse for political gains and then misrepresenting facts through media is the ultra-Communist strategy, which is perfectly used in this case. Mentors like Arundhati Roy can happily use these forums to propagate anti-India ideology."
The magazine said Indians, irrespective of their caste and religion, have a common heritage and "instead of following the path of divisive ideologies they need to establish a process of dialogue to create an atmosphere of social harmony and learn to march together as a nation."
Another cover story "Poisoning student politics" in the Organiser said this strategy of injecting "divisive" thinking among students can prove dangerous not only for the respective organisations but all for student politics too.
It charged that "hatred and disorder was the message in the student issue raised where misrepresentation of facts were used as convenient tools."
"The soul of student organisation is questioning the government policies, if they are not in the interest of the nation and fight against the administrative tyranny. When these two tools themselves are used for petty political gains, it can be self-destructive to the politics," it said.
In case of Ambedkar Periyar Study Circle controversy, it alleged the issue of disciplinary action by the IIT Madras was turned into curbing of freedom of speech and expression by the Centre.
"Rather than raising the question of caste eradication from all spheres of social life, misrepresenting reformers for spreading hatred is poisonous for the student politics," it said.
Attacking Gandhi, it said the top leader of a party "preaching them disorder and misrepresenting the facts of a nationalist organisation like RSS is another dangerous ploy."