The activists were upset over Shah's reported statement at an election rally in Karnataka that he would assure supply of the Mahadayi river water to farmers in the southern state, if the party was voted to power.
Karnataka and Goa, the riparian states of the Mahadayi river (known as Mandovi in Goa), have been locked in a bitter battle on sharing of the river water, which originates in Belagavi in the southern state.
"We want to convey to Shah that Goa does not welcome his statement on Mahadayi. Both the states are fighting the case before the Mahadayi Water Dispute Tribunal," GSM president Anand Shirodkar told reporters.
He said it was a "symbolic" protest to convey their message to Shah.
The police stopped the protesters about 300 metres from a stadium close to Panaji, where Shah was to address the BJP workers.
The river water sharing issue is pending before the Mahadayi Water Dispute Tribunal.
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