The board has taken such an action for the first time, said an official.
The village panchayat of St Cruz, on the outskirts of Panaji, was fined after a local social worker complained about the practise of burning garbage in open and the board carried out an inspection.
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The board last week instructed the North Goa Collector to recover the fine amount.
GSPCB had sought a clarification from the panchayat. The panchayat failed to file its reply.
The National Green Tribunal, in an order, has prohibited burning of waste in open space.