The finding means that it "now seems more likely" that radioactive water from leaking tanks had mixed with groundwater in the area, Jiji press and Kyodo news agency quoted the Tokyo Electric Power Company (TEPCO) as saying.
Many of the tanks were used to cool molten reactors wrecked by an earthquake and tsunami disaster in March 2011.
The well was found to have contained 3,200 becquerels per litre of beta-ray emitting materials, including strontium.
TEPCO also plans to use wells to pump up the groundwater before it seeps into the sea.
But, according to Kyodo news, the latest findings could affect that plan as the nearest pumping well is only 130 metres away from the monitoring site from where the sample was taken.
