A bench of justices B S Chauhan and S Bobde set aside the order of the Madras High Court which had in 2009 transferred the administration of the 1000-year-old Lord Shiva temple to the government.
The apex court passed the order on appeals filed by the temple's priests and BJP leader Subramanian Swamy.
Swamy contended that an attempt was made after Independence to bring the temple administration under State control in August 1951 but the Supreme Court had held that the Podu Dikshitars had a right to administer the temple as a religious denomination.
He contended that if there were allegations of misappropriation of temple's property then it should be dealt with under the provisions of Indian Penal Code and not by taking over the temple administration.
The state government in 1987 had appointed an official to manage the endowments and considerable assets and property owned by the temple.