Karnataka had objected to the Japanese-aided project, meant to supply drinking water to Dharmapuri and Krishnagiri districts bordering the state, on the ground that its share of the inter-state Cauvery water would be affected.
Replying to the issue raised by Ashwath Narayan (BJP), Bommai said government was forced to take legal steps after the Central government failed to intervene in this regard.
Bommai said the government had directed its law department to file a suit in the apex court to resolve the long-pending dispute.
It was not right to go ahead with the project unless and until the border row is resolved, he said.
"We had written a letter to the Centre seeking its intervention on the matter," he said.
Hogenakkal is part of Koothapadi panchayat village within the Pennagaram sub-district of Dharmapuri district, but the ownership of a piece of an uninhabited island near the waterfall is contested by Karnataka. This has further strained ties between the two states.