The committee will be headed by Director General of National Museum C V Ananda Bose and will also consist of representatives of the Archaeological Survey of India and Reserve Bank of India.
A bench headed by justices R V Raveendran and A K Patnaik said that the expert committee would submit its report only to the apex court.
The court also directed that the entire process of unearthing be video graphed and photographed. The apex court passed the order on an application filed by Marthanda Varma and his other family members.
They challenged the Kerala High Court order of taking over of the assets and management of the shrine by the state government.