Mohamed Osman Mohamud, also known as Mohamed Garfanje, was arrested on Monday during a raid on a house where he was staying.
He is considered to rank second in the nation's piracy hierarchy.
Police said several other people were apprehended in the operation, including pirate commander Mohamed Dahir Farah.
Security forces seized weapons and ammunition, including rockets, in the raid, which was part of a city-wide disarmament operation.
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