Fisheries officials said all arrangements have been put in place to enforce the ban. Patrol boats will be deployed by the department to ensure that there are no violations.
Owners of trawling boats have been asked to dock their boats by midnight.
Even though the centre had decided to impose a uniform 61-day fishing ban from June 1, the state government had decided to allow its fishermen to operate till June 14 midnight.
Fishermen in Kerala had protested the centre's decision on a 61-day ban to protect marine wealth and certain provisions of the Meenakumari report on deep sea fishing in coastal areas.
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Instead of preventing fishermen, the government should stop foreign trawlers in the waters, he said.
The central government had issued a notification in April
this year imposing uniform fishing ban for 61 days in the exclusive economic zone from June 1 to July 31.
Kerala Chief Minister Oommen Chandy had met Prime Minister Narendra Modi in New Delhi last month and discussed the issues concerning fishermen, two days after Congress vice president Rahul Gandhi criticised the centre's decision to extend ban on trawling.