The sea surge under the influence of Cyclone Amphan in the Bay of Bengal led to inundation of habitations at Pudimadaka, 50 km from the city, on Wednesday.
Even as the cyclone spared the Andhra Pradesh coast, the sea remained very rough under the influence of extreme weather system, with strong waves lashing the Visakhapatnam coast.
It created panic among the villagers at Pudimadaka as tidal waves damaged several boats, said fishermen youth activist Arjili Dasu.
Pudimadaka is one of the largest fishing villages in the State with 18,500 residents.
With the sea surface remaining very rough along the coast, fishermen have been advised not to venture into the sea.
They have also been told to anchor the vessels at a safe distance from the sea.
A Fisheries Department official said a few boats suffered minor damage due to sea surge at Pudimadaka which is located on the beachfront. Gales also lashed the village.
As the annual fishing ban is under way, all the motorised boats have stopped venturing into the sea. Only the catamarans and other traditional boats are permitted to go for fishing in the sea.