The Centre's move has drawn flak from social activists and also the opposition Congress.
Parrikar said rights over these rivers are vested with the Inland Waterways Authority of India (IWAI) through an act of Parliament.
"If you don't sign an MoU with the IWAI (for development of the rivers), powers over these rivers will remain with the Centre which has already declared them as national waterways," he said here.
It is wrong to say these rivers in Goa have been nationalised, Parrikar said.
He was addressing a gathering of MLAs, other elected representatives and NGOs over the issue of according national importance to six rivers from Goa.
A handful of protesters held a demonstration outside the venue where the event was organised.
Congress leader Ravi Naik said the state should not go ahead with the signing of MoU with IWAI.
He suggested the state should generate funds on its own to develop these rivers rather than getting them from the Centre under the proposed MoU.
The Union government has declared certain stretches in six rivers Mandovi (44 km), Zuari (50 km), Cumbharjua (17 km), Chapora (33 km), Mapusa (27 kms) and Sal (14 km) as that of "national importance".
Parrikar said rights of fishermen and other communities will be safeguarded under the MoU. The coastal regulation zone norms will remain in force.
"We will take local communities into confidence before dredging the rivers. We will dredge them only if required," he said referring to worries expressed by fishermen over their livelihood getting affected if the rivers are dredged.
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