The capital Tokyo and several nearby municipalities last week said they had detected radioactive iodine-138 levels that made their tap water unsafe for infants, although the contamination has dropped off since.
The health ministry warned at the weekend that fresh rainfall could capture radioactive elements that have escaped from the stricken Fukushima plant, and channel them via rivers and dams into drinking water supplies.
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"As the radioactive substances increased in Tokyo after rainfalls, the ministry has asked operators of water purification plants nationwide to take possible countermeasures," a ministry official told AFP Monday.
Steps included "stopping the intake of river water after rain and covering purified water pools with plastic sheets," the official said.
"The ministry has instructed that such measures be taken only to the extent where they do not disrupt a stable potable water supply."
The ministry also advised the plants that they can use a powdered carbon substance in the purification process to reduce radioactive materials.
Japan's meteorological agency forecast that it may snow or rain Tuesday afternoon in parts of Fukushima prefecture, where the tsunami-stricken plant is located, and in neighbouring Ibaraki prefecture.
