The Rohingyas allegedly fled to India after violence in the Western Rakhine State of Myanmar.
Rohingya, described by the United Nations as the world's most persecuted people, have faced heightened fears of attack since dozens were killed in communal violence in 2012.
The Centre had recently said the Rohingya Muslims were illegal immigrants and pitched for their deportation.
The Supreme Court, however, asked the Centre not to treat the Rohingya Muslims issue as a national security issue but consider it as a humanitarian and human rights issue.
The top court, while hearing plea filed by two Rohingya Muslims, also directed the Centre to strike a balance between human rights and national security when it comes to dealing with refugees in the country.(ANI)