Police said the 1400-year-old temple had many ancient and precious idols.
The consecration of the temple was performed in 1959 by the 'Dharumpura Adheenam' which was administering the shrine.
A part of the temple was in a dilapidated condition.
After poojas, the temple was closed at eight PM yesterday and opened early this morning when the Nataraja idol was found missing, police said.