"Even the country of their origin has accepted them as its citizens", Chief Justice Ranjan Gogoi and Justices S.K. Kaul and K.M. Joseph said, adding that they would not like to interfere with the government's decision.
The men were in Silchar central prison in Assam since 2012 for illegally crossing the border in violation of the Foreigners Act.
Separately, Shirin Sharmeen Chaudhury, Speaker of Parliament of Bangladesh - where nearly a million Rohingyas have taken refuge after fleeing attacks by Myanmar's security forces - asked countries to exercise caution and ensure the safety of the men being deported before sending them to Myanmar's Rakhine state.
"Seven Myanmarese nationals have been deported today".
The deportation came after a last-ditch effort by advocate Prashant Bhushan for an urgent hearing of a PIL in the Supreme Court to restrain the government from deporting Rohingya refugees failed.
The plea, therefore, was dismissed by CJI Gogoi's Bench on these grounds.
Almost 200 Rohingya are known to be detained in India on charges of illegal entry, Achiume said.
"We will drive them from this border point and drop them 100 kms from here, and after that it is their responsibility to go to the Rakhine state of Myanmar", Aung Myo, deputy director of immigration in Myanmar's Tamu border district told reporters during a televised press briefing.
The seven men deported on Thursday had been interred in a detention centre in India's Assam state.
ASG Tushar Mehta tendered an affidavit and said in court that the Embassy of Myanmar was ready to give Certificate of Identity (COI) to the people.
He said that after the genocide which has happened in Myanmar in which over 10,000 people have died, lakhs of Rohingya have migrated to Bangladesh and India.
"Illegal immigrants will be identified and repatriated", said Rijiju.
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 time Rohingya immigrants have been sent back to Myanmar from India.
More than 700,000 Rohingya fled to Bangladesh after an army crackdown in Myanmar a year ago.
The Rohingyas are stateless and suppressed minorities residing in the Rakhine province of Myanmar. It had also asked state governments to identify and deport them.
The deportation exercise was carried out by the government despite the United Nations Special Rapporteur on racism flagging concerns that their "forcible return" could lead to "refoulement" - the forcible return of refugees or asylum seekers to a country where they are liable to be subjected to persecution - which is in violation of global law.
An additional 40,000 Rohingya refugees are thought to be in India, though only 18,000 are registered with the United Nations Refugee Agency, UNHCR.