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Implemented to protect fish stocks during the monsoon breeding season, the ban was enforced from June 9.
The weather body issued a red alert in Malappuram, Kannur and Kasragod on Monday.
Fisheries control rooms will operate 24 hours a day in coastal districts.
The weather agency on Saturday sounded an orange alert for Thiruvananthapuram, Kollam, Pathanamthitta, and Idukki.
The indiscriminate catch of juvenile fish by mechanised vessels to supply to fish manure factories in neighbouring states was one reason that compelled the authorities to effect the ban in 2017.
The ban was not applied to smaller inboard and traditional boats.
The weather agency issued a red alert in Ernakulam, Idukki, Malappuram and Kozhikode.
India’s demand to continue the fisheries subsidies for the small-scale fishermen, for another 25 years, was rejected.
The ban, which is imposed every year during the monsoon season to ensure the prosperity of the marine stock, prohibits fishing by trawling off the Kerala coast during the period.
The ban is intended to enhance marine fish stock and improve their habitat.