Granted more time to all the parties to argue, the court posted the matter for further hearing on November 21.
The Rohingya approached the Supreme Court after India's junior home affairs minister, Kiren Rijiju, told Parliament in August that state governments had been asked to identify and deport people who entered the country illegally, including Rohingya.
However, it also allowed petitioners to approach it in case of any contingency.
In a strongly-worded observation, the Supreme Court reminded the government that it has multiple responsibilities, and must balance national and humanitarian values.
The apex court also said the government should be sensitive to the Rohingyas and can not be oblivious to the plight of innocent women and children, reported CNN-News18.
During the brief hearing, the bench suggested to the Centre not to deport the Rohingya Muslim refugees, but Additional Solicitor General (ASG) Tushar Mehta requested that it should not be written in the order as anything coming on record will have an global ramification.
Close to 40,000 Rohingya Muslims live in India after fleeing Myanmar over the past decade.
"We have to strike a balance".
The refugees are fleeing a military operation in which security forces and Buddhist mobs have killed men, women and children, looted homes and torched Rohingya villages.
Till then the court has ordered status quo in the issue.
On Thursday, a group of eminent personalities urged Prime Minister Narendra Modi to not deport Rohingya refugees and asylum-seekers, saying a proposal that the entire community is a threat to national security is based on "false assumption". They claimed that they have taken refuge in India after escaping from Myanmar due to widespread discrimination, violence and bloodshed against the community there.
Almost 15,000 have received refugee documentation, according to the United Nations, but India wants to deport them all.
The UN's human rights chief has criticised India's decision as lacking "basic human compassion".