Mohammad Salimullah, a Rohingya Muslim who is seeking asylum in India, claimed before the top court that the Constitution provides equality and protection to both citizens and foreigners alike.
Mr Salimullah denied Rohingya Muslims are a threat to India. "Rohingya are not involved in any act of militancy. They are a fleeing persecuted ethnic minority whose only claim is to peaceful asylum," he told the court.
Home Minister Rajnath Singh had said Rohingya Muslims living in India are not refugees but illegal immigrants from Myanmar, and that objections to deport them are baseless since Myanmar has expressed its willingness to take them back.
Mr Singh had also questioned organisations that are objecting to deportation of Rohingya Muslims. "When Myanmar is ready to accept them. I don't know what the objection is," he had said.
The Rohingya petitioner, however, told the top court that deportation would violate human rights and India's commitment to international law on refugees.
The Supreme Court will hear Mr Salimullah's plea on October 3.
The government has said it can deport Rohingya Muslims and has asked the top court not to interfere.
Human rights monitors say the number of Rohingya who have arrived in neighbouring Bangladesh from Myanmar's Rakhine state is 1.5 lakh.