The RFID card is mandatory for the fishermen to venture into the sea for fishing.
State fisheries secretary Govind Jaiswal yesterday issued the show cause notice to the department's director, Sharmila Monteiro.
"It has been observed that RFID cards to fishermen are supposed to be issued before August 1, 2017 as the season starts, but it has been delayed by the department," reads the notice signed by Jaiswal.
"The minister of fisheries has taken a serious note of the matter and instructed to issue the show cause notice," Jaiswal said, asking Monteiro to reply within 24 hours.
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Goa's Fisheries Minister Vinod Palyekar had then said that an inquiry will be conducted into it.
He said that a similar delay was witnessed during the last two years also.
The fishing season in the state resumed from July 31 after a 61-day ban during the rainy season.
Fishing constitutes a major industry in the coastal state which has seven jetties, where the catch lands before either being exported or sold in local market.