He was speaking at a seminar organised by the National Human Rights Commission in New Delhi.
"Some people have entered India in an illegal fashion and now there is talk of their human rights".
The Centre said that since India is not a signatory to the Convention Relating to the Status of Refugees, 1951, the obligations concerned to non-refoulement is not applicable.
The government told judges it has received information on Rohingya involvement in plots by IS and other "extremist groups" to ignite communal and sectarian violence in India.
The bench then fixed the PIL and several other interim applications, seeking to intervene in the case for hearing at 2 PM on October 3.
"Whatever government will do, will be in nation's interest", Rijiju told reporters ahead of the Supreme Court hearing on Rohingya Muslims who have fled from Myanmar and a large number of them are in India. It is completely within the executive policy how to deal with illegal migrants like Rohingya Muslims.
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However, an Indian External Affairs Ministry spokesman last month said there were indications that around 40,000 were staying illegally, largely in Jammu, Hyderabad, Haryana, Uttar Pradesh, Delhi and Rajasthan, and that the government was intent on deporting them.
It said the plan to deport Rohingya refugees was a policy decision and the court should desist from interfering. In the past four weeks, over 420,000 Rohingya have fled to Bangladesh, and satellite imagery and heat sensors analysed by Human Rights Watch have shown more than 228 villages burned to the ground in northern Rakhine state.
The government had also said if allowed to stay, the Rohingya refugees would exhaust natural resources meant for Indians that could culminate in hostility towards them and lead to social tension and law and order problems.
Bangladesh struggles with more than 410,000 Rohingya who have flooded across the border since August 25 when the military in Buddhist-dominated Myanmar launched a crackdown on the minority Muslim group. The visibly emaciated Rohingya we see in moving visuals do not look like radicals.
Rohingya, who are predominantly Muslim, are reviled by many in Buddhist-majority Myanmar.
Nobel Prize victor Aung San Sui Kyi, the chancellor and de-facto ruler of Myanmar - once a darling of the global community has got a bad name for the treatment meted out to Rohingyas but the fact of the matter is that she has no control over the military.