The apex court has fixed hearing on the matter for October 3 after a petition challenged the government's decision to deport Rohingyas who have fled Myanmar after a military offensive in Rakhine state.
"The court has no business to interfere in such matters of what they call illegal immigrants or illegal migrants", the government said in an affidavit.
India's government said Monday that it has evidence there are extremists who pose a threat to the country's security among the Rohingya Muslims who have fled Myanmar and settled in many Indian cities.
Earlier, the Union Ministry of Home Affairs (MHA), in its affidavit, had termed the Rohingyas as "illegal" immigrants and alleged that some of them were part of a "sinister" design of Pakistan's ISI and terror groups such as the ISIS.
The lawyer representing the Rohingya said the decision was discriminatory.
The spokeswoman said Facebook was aware that Rohingya activists were using the site to draw attention to the violence, and that it meant to allow non-graphic content to remain online.
The findings of the commission, which were released recently, among others, stated that the government of Myanmar must scrap restrictions on movement and citizenship of the Rohingya in order to avoid fuelling "extremism". "Some of the Rohingyas with militant background are also found to be very active in Jammu, Delhi, Hyderabad and Mewat and have been identified as having a very serious and potential threat to the national security of India", he said in a written statement to the court.
The social network is a key tool in the information war taking place over violence in Myanmar's Rakhine state, which has driven more than 4,20,000 Rohingya Muslims from the country and sparked United Nations accusations of military-led "ethnic cleansing".
"I am sure Myanmar will take positive steps to take back the Rohingyas". No Rohingya has got asylum in India nor have they applied for it.
Human rights group Amnesty International has blamed Myanmar's State Counsellor Aung San Suu Kyi and the country's government for "burying their heads in the sand over the horrors unfolding in Rakhine State".