The castle, built about 500 years ago in the Ryukyu Dynasty, was designated Japan's national treasure in 1933. It was nearly completely destroyed in a battle during World War Two but was extensively restored using photographs and drawings taken before the war, reopening in 1992.
The complex reopened as a national park in 1992.
Almost a dozen fire engines were dispatched to the scene, Kyodo news agency said, with unconfirmed reports suggesting other buildings in the complex may also have caught fire.
It was reconstructed after the warfare and totally redone within the 1990s, CNN reported.
In addition to the main hall, the north and south halls have been destroyed, NHK said. The three halls were not equipped with sprinklers as their installation was not mandatory, according to the local fire department.
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Officials' preparations related to an ongoing festival at the site had been ongoing until 1:00 am, hours before the blaze erupted. None of them were believed to be present when the fire broke out, according to the police.
The blaze started before 3am on Thursday morning. This work was based on detailed documentation of the original and was noted in the World Heritage inscription as respecting the authenticity.
And the Olympic torch relay for next year's Tokyo Summer Games was due to pass by the site as it travels around the country in 2020.
"We have lost our symbol".
UNESCO Director General Audrey Azouley expressed her sympathy.
The disaster saddened locals as the smell of burning and white smoke filled the air in residential areas near the site.
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Temple buildings in the castle complex were also destroyed and local residents were evacuated. "But I also feel strongly that we must reconstruct Shuri Castle, a symbol of the Ryukyu Kingdom filled with our history and culture".
The blaze started before 3am on Thursday, with the cause unknown as yet.
The castle uses both Japanese and Chinese architectural styles, underlining the unique characteristics of the Ryukyu Kingdom, which long served as a transportation hub connecting China and Japan.
The castle was previously burned to the ground by USA forces during WWII.
The castle is situated on a hill that overlooks the capital of Okinawa. "The damage is immeasurable".
World heritage site Shuri Castle has been destroyed by a fire.
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