The cause of the fire was not immediately known.
The annual Shuri Castle Festival had started Sunday and events scheduled there this weekend are canceled.
Residents close to the fort have been being evacuated from the world after the flames broke out, reviews mentioned.
Television footage showed large orange flames engulfing the castle before sunrise, with daylight revealing the extensive damage done to the site. Some people were crying.
The mayor of Naha, Mikiko Shiroma, said: "I am extremely saddened by this". "My heart is broken", he said. A third main structure Nanden, or south temple, was also burned down later.
It has been destroyed and rebuilt after many fires - most recently in the Battle of Okinawa in 1945.
The complex burned down after it was bombed by United States forces during the Battle of Okinawa in 1945. This fortress is a UNESCO world heritage site and it has enormous cultural and historic importance for the people of Okinawa.
Shuri castle is a key part of a complex dating back to the Ryukyu kingdom, and is believed to have been in use from around the 1400s.
It was reconstructed after the warfare and totally redone within the 1990s, CNN reported.
More than 10 fire engines were dispatched to the scene.
"It started at the main temple and looks to be spreading fast to all the main structures".
Shuri Castle on Fire.
Kurayoshi Takara, a historian at the University of the Ryukyus who helped reconstruct Shuri Castle, said he was speechless when he saw the fire.
"I feel like someone I was close to has passed away", said Tokiko Taira, 69, with tears in her eyes. "It has taken more than 30 years and it was a monument of wisdom and effort of many people".
Japan is dotted with historic castle complexes, most of which are careful reconstructions of original buildings.
UNESCO Director General Audrey Azouley expressed her sympathy.