Photos and videos shared online showed blood-red water flowing through the rivers and port areas of Nago city, on the island of Okinawa, a destination better known for emerald waters and sandy beaches.
But a local brewery urged people not to worry, saying there had been a leak at one of its plants and that the discoloured water posed no danger to humans or marine life.
“We believe it was caused by the leakage of propylene glycol – a food additive listed in enforcement regulations of the Food Sanitation Act – contained in cooling water used to cool our factory facilities. We believe the leaked cooling water flowed into a river through a rain gutter, causing the sea to turn red,” Orion Breweries said.
It added that the leak had been “plugged” by 9.30am on Tuesday (local time) – though a spokesperson for the Japanese Coast Guard told CNN the seawater near the brewery was still red as of Wednesday morning.
Propylene glycol is commonly used in the food, cosmetics and pharmaceutical industries.

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The US Food and Drug Administration (FDA) classifies it as “generally recognised as safe” for use in food.
Orion Breweries also apologised for causing “inconvenience and enormous trouble and worry” and said it had launched an investigation and was working with authorities to take “countermeasures”.
Roughly 640 kilometres south-west of mainland Japan, Okinawa is Japan’s fifth largest island and has been a strategic location for US armed forces since the 1945 Battle of Okinawa in World War II.
The island is today a popular tourist destination for international travellers.
News of the red seawater amused some social media users but left others questioning if the water was safe.
One Twitter user said crowds of people had gathered to look at the red sea. “What is this? Is our ocean ok? The seawater is so red,” he tweeted.