Japan's probe at the Yokota Air Base followed a US notice two months ago that water containing PFOS -- classified by the World Health Organisation as "possibly carcinogenic to humans" -- had spilled from the site.
PFOS is part of a large group of man-made chemicals known as PFAS, sometimes called "forever chemicals" because they do not degrade easily, experts say.
The US military informed Tokyo in October that the PFOS-laced water had leaked from an area of the base where a fire-fighting drill was being carried out, Fumitoshi Sato, deputy chief cabinet secretary, told reporters.
"This inspection was realised in response to the fears and concerns harboured by local residents, and we will continue to work together with the US side," Sato said.
Officials including from the defence ministry and Tokyo's metropolitan government visited the site on Friday, he said.
"PFAS is a shared concern applicable to military and civilian industrial activities across Japan regardless of nationality," the Yokota Air Base's public affairs office said in a statement to AFP.
"We remain committed to protecting the health of our personnel, their families, and the surrounding communities in which we live and serve," it said, adding that it will observe all relevant agreements and obligations and closely coordinate with the Japanese government "towards sustainable solutions."
America's military presence in Japan has frequently stoked local discontent in the past, with everything from noise to pollution to helicopter accidents.
This frustration is perhaps most evident on the southern island of Okinawa, which despite comprising just 0.6 percent of Japan's landmass, hosts the vast majority of the country's US military bases.
Okinawa is located east of Taiwan, a flashpoint for tensions between the United States and China.
Earlier this month, the United States began relocating thousands of Marines from Okinawa, with an initial "detachment of approximately 100 logistics support Marines" transferred to the US island territory of Guam.
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