Promoted to commodore, Keppel became second-in-command of the East Indies and China Station, with his broad pennant in the frigate HMS "Raleigh", in September 1856. HMS "Raleigh" was lost on an uncharted rock near Hong Kong, and, although Keppel was subsequently court-martialed, he was honourably acquitted for the loss of the ship. He then transferred his pennant to the sixth-rate HMS "Alligator". After commandeering the chartered steamer , he commanded the British squadron, which consisted of the "Hong Kong" and seven gun boats, in the action with Chinese pirates at the Battle of Fatshan Creek in June 1857 when he sank around 100 enemy war-junks. For his part in this action Keppel was advanced to Knight Commander of the Order of the Bath on 12 September 1857. He also took part in the capture of Canton in December 1857 during the Second Opium War.