Tokyo Electric Power Co (TEPCO) said tests showed the highly toxic strontium-90, a by-product of nuclear fission that can cause bone cancer if ingested, was present at levels 30 times the permitted rate.
The firm said it had also detected tritium, a radioactive isotope of hydrogen used in glow-in-the-dark watches, at around eight times the allowed level.
"From groundwater samples we collected, we detected 500,000 becquerels per litre of tritium, that is very high," a TEPCO official told a press conference.
Subsoil water usually flows out to sea, meaning these two substances could normally make their way into the ocean, possibly affecting marine life and ultimately impacting humans who eat sea creatures.
However, a TEPCO official said seawater data showed no abnormal rise in the levels of either substance.
He added the company believed the groundwater was largely contained by concrete foundations and steel sheets, and any gaps were being plugged with a material known as "liquid glass" that would solidify, forming a physical barrier.
Workers used tonnes of water to cool the melted cores of the reactors and TEPCO is having to store this radioactive water on-site. However, reports continue to emerge of leaks in storage pools, tanks and pipes.
Critics say improvised fixes put in place at Fukushima since the disaster leave it vulnerable to problems and at the mercy of nature, with no immediate end in sight.
In a separate move, the Nuclear Regulation Authority (NRA) today officially decided on the nation's new safety requirements for reactors.
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