The plea has been filed by two Rohingya immigrants, Mohammad Salimullah and Mohammad Shaqir.
The Center said intelligence inputs show that illegal Rohingya immigrants in areas like Jammu, Delhi, Hyderabad and Mewat have links with terror organisations while some are involved in an organised influx of illegal immigrants from Myanmar through agents and touts. However, the Narendra Modi-led government has argued that deportation of Rohingyas - a policy decision taken in the interests of citizens, can not be challenged under Article 32 by non-citizens.
The Supreme Court on Monday fixed October 3 as the date to hear a plea challenging the deportation of Rohingya Muslims to Myanmar after Centre told the apex court that it would file its response in the matter during the day.
A draft affidavit that had leaked on Thursday had termed Rohingya Muslims a "serious threat to national security".
One of the petitioners, who said he has been in India for at least five years, said he was hopeful that the court would support the refugees.More news: Three injured as stand collapses in County Durham
Referring to the inputs of security agencies, the affidavit said the "Rohingyas figured in the suspected sinister designs of ISI/ISIS and other extremists groups who want to achieve their ulterior motives in India".
"There is also a serious potential and possibility of eruption of violence against the Buddhists who are Indian citizens and who stay on Indian soil by the radicalised Rohingyas", the affidavit adds further.
"Involvement of some of these illegal migrants has been noticed in criminal activities including obtaining fraudulently Indian identity documents and fake currency", said an internal note of the ministry. Minister of State for Home Affairs Kiren Rijiju had said they were illegal immigrants, even those registered with the United Nations High Commission for Refugees.
Around 40,000 such refugees are said to be residing in India.
The government of Hindu nationalist Prime Minister Narendra Modi said last month it had asked state authorities to identify and deport Rohingya living in their territory.
The Indian government has contended that there was an organized Rohingya Muslim influx which started in 2012 and their number is around 40000 now.
India is not a signatory to Convention Relating to the Status of Refugees, 1951 and Protocol Relating to the Status of Refugees, 1967, and is hence not bound by their provisions.