The retired Chief Justice of India said the human rights body was helping the Rohingya on "humanitarian grounds" as they faced persecution in Myanmar.
"The Home Ministry has clarified its position through its affidavit (in Supreme Court) that these are illegal immigrants and they will be deported".
Contesting the Central government's stand that they being foreign nationals enjoyed no protection under the Indian Constitution, Rohingya refugee Mohammad Salimullah, who has moved the top court, seeking its protection from being deported said that protection under Article 14 - guaranteeing equality before law and Article 21 - guaranteeing protection of life and liberty was available to both Indian citizens and non-citizens alike.
Rohingyas are minority Muslims in western Myanmar and have been fleeing their homes following an army crackdown on their villages that has left hundreds dead.
The NHRC, quoting a report in The Hindu on the Centre's plan to deport the Rohingya, recently issued a notice to the Centre.
"At present, around 40,000 Rohingya are living in the country".
"If (Rohingyas) are deported back to their country, we see it as a violation of human rights".
"The government can not make a blanket claim that all Rohingya refugees have terror links and there being a fear of them being radicalised by terror recruits operating in India".
The petitioner said that they fled, in the wake of their persecution on the grounds of their religion, and argued that they were entitled to all protection under the global conventions on refugees and treaties.
He said Rohingyas who had take refuge in Bangladesh had gone back in 1977 under United Nations monitoring but were forced to flee again by the Myanmar government.
Moreover, there was not a single FIR registered against Rohingyas in any matter that would jeopardise national security, they said.
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".
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