The fishermen are demanding a higher compensation package.
The protest, held under the aegies of the Latin Catholic church, also wanted the Centre to declare the calamity as a national disaster and urged Prime Minister Narendra Modi to visit the affected areas.
Ninetyfive persons are still missing, according to official sources.
The state government has announced a relief package for the affected victims, which among other things included Rs 20 lakh each to the families of those who had lost their lives in the cyclone.
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Search operations will continue as 95 more persons have to be accounted for, defence sources said.
The protesters waving black flags and photos of the dead and missing fishermen walked about two km from Palayam to Raj Bhavan raising slogans, bringing the traffic to a standstill on the busy stretch.
They also carried a symbolic coffin.
Addressing the gathering, Latin Catholic church head Archbishop Soosai Pakiyam, who led the march, said it was a matter of grave concern that the authorities "are unable to come out with the exact number of fishermen missing in the cyclone."
The state government has also demanded a financial assistance of Rs 1,834 crore from the Centre in view of the loss suffered due to the cyclone.
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