Pol Lt Col Udom Phetcharat of the Phuket City Police was informed of the blaze at about 5am.
Police and firefighters soon arrived at the scene, on a canal near the Asia Marina Pier in Moo 1, Ratsada.
Marine Police have yet to confirm who owns the boats.
Officers inspected the boats, but preliminary inspections were unable to determine the cause of the fire.
Forensics investigators have been called in as the investigation continues.
Two fishing boats, the Thong Charoensap 32 and the Yutuna No. 3, were also destroyed by fire in the Klong Noi area nearby in August.