Reports quoted the Union Minister as saying that "every country will decide the course of action based on its foreign, security policy and balance of population".
"The court has no business to interfere in such matters of what they call illegal immigrants or illegal migrants", the government said in an affidavit. He said the refugees were entitled to protection of their fundamental rights under Article 12 and 14 of the Indian Constitution.
He told news agency ANI that if India decides to not allow Rohingyas then the worldwide community can not ask it to take allow refugees.
The centre said that it has inputs from intelligence agencies about links of some Rohingya Muslims with Pakistan's ISI and Global terror networks such as the Islamic State.
The situation in Myanmar, a mostly Buddhist country, has generated criticism of the governing party's leader, Aung San Suu Kyi, who addressed the crisis publicly for the first time Tuesday in a nationally televised speech from the capital, Naypyitaw.
The BJP-led government's argument was in response to a petition filed by two Rohingya refugees challenging the Centre's decision to deport an estimated 40,000 people of the community living in India.
"It is submitted that continuance of Rohingyas' illegal immigration into India and their continued stay in India, apart from being absolutely illegal, is found to be having serious national security ramifications and has serious security threats", it said.
More than 400,000 Rohingyas have fled to Bangladesh since August 25, in the wake of a violent military offensive launched after hundreds of Rohingya rebels assaulted police posts.
Pointing that the influx of Rohingya refugees from Myanmar started in 2012-13, the Centre said there was an organised "influx of illegal immigrants from Myanmar through agents and touts" facilitating their entry into India through West Bengal, Tripura and Assam. Rohingya activists say many families have lived in Myanmar for years.
Summary: With the providing assistance to Rohingya refugees in Bangladesh, India has made it clear that New Delhi is ready to provide support on humanitarian ground.
"We have always condemned the attacks (on Myanmar security forces) and we will continue to do so in future", he said.
He said that India had sent a large quantity of relief material to Bangladesh but claimed that even Bangladesh had security concerns regarding Rohingyas.