A bench comprising justices T S Thakur and P C Ghosh said that the compensation amount has to be paid within four weeks.
The bench also admitted the petition challenging the order of the Gauhati High Court holding as valid the appointment of commission of inquiry to go into the circumstances leading to the ghastly incident.
In November, the judicial inquiry report on the issue was handed over to the apex court revealing the "brutal and merciless" torture of the girl by the Assam Rifles team.
Manorama was picked up by the troops of 17th Assam Rifles on the intervening night of July 10-11, 2004 from her home in Imphal East district.
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She was found dead with multiple gun shot injuries at Ngariyan Yairipok Road, two km away from a police station.
According to the inquiry report, the two FIRs filed by the 17th Assam Rifles claimed Manorama led them to recover Kenwood and Chinese grenades and an AK-47 rifle. It further said that she had tried to escape and was shot in the legs.