Six crew members with more than 300 kgs of a banned substance were apprehended in the second such incident in the last three months.
The boat had gone missing after capsizing on December 7 with seven fishermen onboard, who are still missing, coast guard officials said.
Earlier, there was a legal loophole using which the vessel companies could sue the Coast Guard for detaining ships without any authorisation.
The Centre has dropped plans to set up a Coast Guard Academy in Kannur.
Under the impact of strong winds, the boat drifted towards Bangladesh whose Coast Guard personnel caught the fishermen and took them into their custody.