The boat was bound for the violence-hit north, where a military campaign sparked by militant attacks has forced hundreds of thousands of Rohingya Muslims to flee the country.
The government's argument was in response to a petition filed by two Rohingya refugees challenging any Indian decision to deport an estimated 40,000 people of the community who fled alleged persecution in Myanmar.
Police vehicles and a crowd of people are seen near the jetty where a Red Cross boat loaded with humanitarian aid docked, in Sittwe, western Myanmar, on Wednesday.
A truck filled with aid for Rohingya Muslim refugees in Bangladesh veered off a road and fell into a ditch Thursday morning, killing at least nine aid workers, hours after another aid shipment in the refugees' violence-wracked home state in Myanmar was attacked by a Buddhist mob.
"Later, the Bengali population exploded and the aliens tried to seize the land of local ethnics", Min Aung Hlaing said, according to his office's Facebook page.
The prime minister laid out a five-point plan that called for the protection of the Rohingyas in "safe zones that could be created inside Myanmar under United Nations supervision".
The Centre's affidavit, filed in the apex court Registry, said the fundamental right to reside and settle in any part of the country is available to citizens only and illegal refugees can not invoke the jurisdiction of the Supreme Court to enforce the right.
ICRC spokeswoman Graziella Leite Piccoli confirmed to the BBC that there had been an incident, but could not confirm other details.
"We are explaining to the community members who approached the boats about the activities of the Red Cross", said Maria Cecilia Goin, a communications officer at the ICRC Yangon.
They have always been ostracised in Myanmar, where they are considered illegal immigrants and face severe restrictions.
The exodus followed a military crackdown in response to coordinated attacks by Rohingya militants on security forces. Those who died were workers helping to distribute supplies, reports said.
Myanmar leader Aung San Suu Kyi, in her first address to the nation on the crisis on Tuesday, said Myanmar was ready to start a verification process to take back refugees, under a 1993 arrangement with Bangladesh.
Myanmar's government is facing mounting global criticism for its response to the Rohingya crisis.
Earlier on September 18, the Centre had filed an affidavit in the apex court on the deportation of Rohingya Muslim from India while terming them a threat to national security.
He said not just Muslims but other minority groups had fled, and security forces had been told to "take full measures to avoid collateral damage and the harming of innocent civilians".
Media captionWatch: Who are the Rohingya?
In the US, Vice-President Mike Pence accused the military of showing "terrible savagery" towards the Rohingya, the strongest remarks from the administration yet on the crisis.
He said the violence would "sow seeds of hatred and chaos that may well consume the region for generations to come and threaten the peace of us all".
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