Justice V Chitambaresh issued the order on a petition filed by the senior pontiff of Kashi Math Swami Sudheendra Theertha.
The court said the seer "remains invisible to the court and the police." As many as 234 gold ornaments embedded with diamonds, rubies, emerald etc used for adorning deities in addition to silver articles are to be recovered, it said.
"To do complete justice and maintain credibility of the system, a CBI probe is required," the Court said.
The court also directed Kerala police to hand over files to CBI, New Delhi, for tracing the absconding seer.
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The court had earlier directed CBI to inform whether it was prepared to take over the probe into the disappearance of the seer.
Kerala Police had informed the court that they conducted searches in three states but Raghavendra, who was involved in a dispute with Swami Sudheendra Theertha over the right to be pontiff, could not be located.
The Kerala High Court had earlier directed the police to trace Raghavendra and produce him before the court following a habeas corpus petition in this regard by the followers of Swami Sudheendra Theertha.