India's home ministry said it would confidentially share intelligence information with the Supreme Court showing Rohingya links with Pakistan-based armed groups, in a bid to get legal clearance for plans to deport 40,000 Rohingya Muslims.
The Supreme Court is hearing an appeal lodged on behalf of Rohingya against the deportation plan proposed by Prime Minister Narendra Modi's Hindu nationalist government.
India's home ministry submitted an affidavit to the court arguing the hardline stance was justified by the security threat posed by illegal immigrant Rohingya, hundreds of thousands of whom have fled from Myanmar to Bangladesh, from where many have crossed into India.
Additional Solicitor-General Tushar Mehta told the court the government will provide evidence of Rohingya links with extremist groups and illegal transfers of money at the next hearing.
The lawyer representing the Rohingya denounced the move.
"This is clearly a case of religious discrimination and an attempt to arouse an anti-Muslim feeling," Prashant Bhushan said.
The ministry said the influx of large numbers of Rohingya into India began four to five years ago, long before an exodus that saw more than 400,000 Rohingya flee to Bangladesh since August 25 to escape a Myanmar military offensive that the United Nations has called "ethnic cleansing".