Two Rohingya men moved the apex court against the Centre's proposed plan to deport the 40,000 members of the community now in India to the land of their origin, Myanmar.
They had fled Myanmar fearing execution and discrimination at the hands of the government.
Solicitor General Tushar Mehta argued before a bench headed by Chief Justice Ranjan Gogoi that their primary prayer was to stop any proposal in connection with deportation and let the international laws regarding community rights govern the matter.
Mehta contended that the major question was regarding the exact identity of the community whether they were refugees or illegal immigrants and whether they could be recognized as refugees.
The court observed that it would examine the issue, and asked the parties involved to complete the pleading in the next hearing.
The UNHCR in 2016 registered and recognised the 40,000-odd Rohingyas in India and granted refugee identity cards and their deportation would violate the commitment to international conventions, said the petition.
The petitioners' counsel argued that compliance with international law does not favour the deportation of refugees to a land where they see threat to them and their families.
The court queried the petitioners' counsel to identify formal guidelines and policy decisions in place for granting refugee status.
Senior advocate Colin Gonsalves, representing the petitioners, said the UNHCR conducts extensive inquiry to identify if economic interests was the reason for people to cross over to another country or if they fear execution. Only then refugee status was granted.
According to the 2016 UNHRC report, the Rohingyas faced threat from state security forces and government officials in Myanmar.
Many of the Rohingyas, who fled Rakhine state in Myanmar, are settled in Jammu, Hyderabad, Haryana, Uttar Pradesh, Delhi-NCR and Rajasthan.
The petitions said the constitution guarantees that the Indian state should "protect the life and liberty of every human being, whether citizen or not".
The National Human Rights Commission had issued notice to the Centre on the proposed deportation.
( With inputs from IANS )