Chief Judicial Magistrate of the court at Virudhachalam, Sathik Basha, ordered that the idol of Ardhanariswara be taken in a police vehicle to that temple and moved to a safe room.
He then adjourned the case to October 2.
The other idol of Nataraja will be produced in a court at Ariyalur later this evening.
"This meant the sculpture should have been stolen at a later date. There seems to be no record with Hindu Religious and Charitable Endowments Department about the missing idol and they were not aware of the theft till the smugglers confessed to having stolen it," he said.
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The DSP said the case was filed based on a news report.
Cuddalore District Collector S Suresh Kumar said the administration would lay claim to the Ardhanraiswara idol and embed it near the sanctum sanctums of the Vridhagireeswarar temple at Virudhachalam, from where it was stolen.
They were brought to Chennai by a government carrier from Delhi and later taken to Archaeological Survey of India office.
Both statues were allegedly stolen from temples in Tamil Nadu and their return was sought by India in March.
The Nataraja idol, dating to Chola dynasty of 11th-12th century, was purchased by the National Gallery of Australia in February 2008 for USD 5.1 million from art and antiquities dealer Subhash Kapoor who was then based in New York.
Kapoor, owner of "Art of the Past" gallery in New York, was arrested in Germany and extradited to India in 2012.
He is accused of conspiracy to commit burglary and smuggling from the state antique idols of Hindu deities.
In March, the External Affairs Ministry had through India's High Commission in Canberra made a formal proposal to the Australian Department of Attorney General by forwarding Tamil Nadu police request for return of the idols.