The top court has also transferred the case to Gauhati High Court and said that "it will continue to monitor the case".
"We will take over the responsibility of providing security to them," the court had told the state government in the morning, which was providing protection to the family.
The victim, Irom Roger, was shot dead by Ajay Meetai, son of Manipur's current Chief Minister N Biren Singh, who was then a sports minister in Okram Ibobi Singh's Congress government.
In May, Roger's parents had approached the Supreme Court asking for protection alleging that "the state police was working at the behest of the convict".
The court had then asked the Centre to consider providing security and observed that without any reason nobody has the courage to make allegations against the chief minister and his family. The Manipur government had said it will follow the order.