Of the over 38,630 temples, about 10,000 temples are in dilapidated condition, he told reporters here.
The department failed to protect the temples and properties, which were encroached, Raja said.
Raja urged the state government to act on a court directive, constitute a committee to identify the encroached land and present occupants and come out with detailed report.
On the Punjab National Bank fraud, Raja said the Centre was taking all steps to recover the money from the people involved in the fraud.
Though disappointed by reduction of quantum of water for Tamil Nadu, Karnataka would not be able to play its tactics of "not releasing water" any more by this verdict, Raja said.
He endorsed the views expressed by union minister Pon Radhakrishnan that Tamil Nadu no longer remained a peaceful state but turning out to be a training centre for extremists.