The gas was detected at an underground pit for electrical equipment during a test opening of the venue, said the Japan Association for the 2025 World Exposition.
Organisers in the western city of Osaka barred people from coming near the affected area for about an hour to ventilate it.
The site of Expo 2025, which opens Sunday, was once a landfill. Discarded household waste creates large amounts of methane when it decomposes if left to rot.
Although organisers have previously taken steps to prevent the gas from being trapped, they vowed Monday to increase the frequency of monitoring.
A fence will be installed so that visitors will not come near the affected area, while ventilation will also be improved, they said.
In March 2024, a restroom at the venue under construction caught fire after a spark from welding work triggered an explosion due to methane trapped there.
Expo 2025 will run for six months, involving around 160 countries and regions for a display of their technological and cultural prowess.
The first "World's Fair" to celebrate culture and industrial progress was held in London in 1851, with the Eiffel Tower built for the 1889 edition in Paris.
Now called World Expo, the event is held every five years in different global locations.
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