Appearing for the Centre, Additional Solicitor General Tushar Mehta told the bench, also comprising Justices S K Kaul and K M Joseph, that "the action with respect to the seven individuals is taken in accordance with law as an administrative decision involving diplomatic and other considerations including an overwhelming consideration of national interest".
The seven had been held at the Silchar central prison in Cachar district since 2012 on charges of illegal entry.
Prime Minister Narendra Modi's Hindu nationalist government, which regards them as illegal aliens and a potential security risk, has ordered that Rohingya living in small settlements and slums around the country be identified and deported.
They are likely to be handed over to Myanmar border guards on Thursday, Mahanta said.
Salimullah, represented by advocate Prashant Bhushan, is also the lead petitioner in a 2017 PIL that challenged the Centre's 8 August 2017 order which directed states to identify and deport illegal migrants including Rohingya refugees. The plea was being heard by the bench headed by CJI Ranjan Gogoi.
The Rohingyas, who fled to India after violence in the Western Rakhine State of Myanmar, are settled in Jammu, Hyderabad, Haryana, Uttar Pradesh, Delhi-NCR and Rajasthan. They were handed over at the border town of Moreh in Manipur.
The UN had voiced concern that returning the men ignored the danger they faced in Myanmar, where for decades the Rohingya have been targeted in violent pogroms by security forces. Some have taken refuge in northeast India bordering Bangladesh and Myanmar.
"The Indian government has an global legal obligation to fully acknowledge the institutionalised discrimination, persecution, hate and gross human rights violations these people have faced in their country of origin and provide them the necessary protection", UN Special Rapporteur on racism, Tendayi Achiume, said in a statement.
Bhushan said it is a matter of life and it is the court's responsibility to see that the lives of Rohingya are protected. This is the first deportation of Rohingya immigrants from India to Myanmar.
"The Embassy of Myanmar also requested Ministry of External Affairs for its assistance in repatriation of the aforesaid persons to Myanmar by suitable arrangements made by the Indian Government", the affidavit said.
New Delhi's move has drawn criticism from the United Nations, which said the forced return of the Rohingya violates global law.
Bhushan's argument in the case pertained to the fact that Rohingyas are recognised by the United Nations agencies as a Stateless people and are known to have fled from Myanmar due to fear from persecution.
More than 700,000 ethnic Rohingya fled an offensive by Myanmar troops launched almost a year ago in reprisal for attacks on border posts by Rohingya rebels who took up arms against the ill-treatment of the stateless minority.