Elevated levels of radioactive strontium, which can cause cancer, have been found 250 kilometres from the stricken Fukushima nuclear plant.
The find in the city of Yokohama has heightened fears that radiation has spread further than the Japanese government has acknowledged.
With a half-life of 29 years, strontium-90 accumulates in bones and can cause leukaemia and other types of cancer.
Until now it has not been detected in elevated levels outside a 100-kilometre radius of the Fukushima nuclear plant, which suffered multiple meltdowns after the March earthquake and tsunami.
A total of 195 becquerels of strontium-90 has now been found in sediment on a rooftop in Yokohama.
City officials have started collecting soil samples near the building in an effort to confirm the contamination has come from Fukushima.
