The Centre had earlier opposed the plea saying that the country cannot be the capital for illegal immigrants.
The girl was found at a house in the Rongpur area of Silchar in the Cachar district two years back in an unconscious state under mysterious circumstances.
On March 6, about 168 Rohingyas were shifted to the holding centre after they were found living illegally in Jammu city during a verification drive.
Both the prime ministers reiterated the importance of their safe, speedy and sustainable return to their homeland for the greater security of the region
A bench headed by Chief Justice S A Bobde refused to hear at this stage the intervention application filed by United Nations special rapporteur in the matter.
A bench of Chief Justice Bobde and Justices AS Bopanna and V Ramasubramanian after hearing detailed arguments on the plea said, 'We are closing it for order'.
Lawyer Prashant Bhushan, for the petitioner, said that he is going to submit an important order of the International Court of Justice before the Supreme Court.
Nearly one million of the persecuted Muslim minority -- many of whom escaped a 2017 crackdown that UN investigators concluded was executed with "genocidal intent" -- live here.
The remarks came days after authorities in Jammu sent 168 Rohingyas to jail after they were allegedly found living in the city illegally, officials had said.
Violent attacks allegedly by Myanmar army men have led to an exodus of Rohingya tribals from the western Rakhine state in that country to India and Bangladesh.
last week, one of the most graphic images of the military-led violence in Myanmar flashed across the globe digitally.
Congress Committee president G A Mir also advocated early assembly elections in the union territory and said 'the government run by bureaucrats does not help the people.'
The plea also sought direction to MHA to expeditiously grant refugee identification cards through the Foreigners Regional Registration Office (FRRO) for the Rohingyas in the informal camps.
Following persecution in their country, many of them entered India illegally through Bangladesh and took shelter in Jammu and other parts of India.
India's Permanent Representative to the UN Ambassador TS Tirumurti said that it must be ensured that the recent developments in the country do not impede the progress made so far.