Officials in Toyko say that radiation levels in the city's tap water make the water unfit for babies to drink.
Iodine levels in some areas are twice the recommended safe level.
The authorities have also imposed new restrictions on food from areas affected by leaks from the Fukushima nuclear plant.
The Food and Drug Administration (FDA) in the United States also announced restrictions on certain food imports. 
Levels of radioactive iodine-131 in some areas of Tokyo is 210 becquerels per liter; the safe level for infants in 100 becquerels per litre. 
People have been warned not to give the water to infants, although there is no immediate health to adults.
Workers at the Fukushima reactor 2 have halted work as radiation levels spiked; the UN atomic agency has said radiation is still leaking from the plant. 
The confirmed death toll from the earthquake and tsunami is now 9,079, with 12,645 missing.
But the Japanese government now estimates that more than 21,000 people died.
The cost of damage caused by the disaster is estimated at about 16-25 trillion yen ($197bn-$308bn). 
The Japanese Prime Minister, Naoto Kan, ordered the governors of Fukushima and neighbouring Ibaraki to halt shipments of a range of agriculture goods.
This included green leaf vegetables, broccoli, parsley and untreated milk after they showed radiation levels which were higher than normal. 
The Japanese Cabinet Secretary Yukio Edano told a news conference that importers of Japanese foods should take a "logical stance".
A statement from the FDA said that all milk and milk products and fresh fruits and vegetables from four Japanese prefectures - Fukushima, Ibaraki, Tochigi and Gunma - will be stopped from entering the United States.
Food and fish retailers are increasingly worried about the effect the crisis will have on their livelihoods.
The sudden halt to work at reactor 2 was a reminder of the challenges still facing emergency workers at the nuclear sites.
 Lighting has been restored to the control centre of reactor 3, hours after power cables were connected to all six reactors for the first time. 
The Fukushima Daiichi plant's operators, Tokyo Electric Power (Tepco), said engineers will try to power up water pumps to reactor 3 some time on Wednesday.
However, they said restoring power to all the reactor units could take weeks or even months.
On Tuesday, an International Atomic Energy Agency (IAEA) senior official, James Lyons, said he could not confirm that the damaged reactors were "totally intact" or if they were cracked and leaking radiation.
"We continue to see radiation coming from the site... and the question is where exactly is that coming from," Mr Lyons told a news conference.
The government has evacuated tens of thousands of people within a 20km (12-mile) radius of the plant and told residents 10km beyond that to stay indoors. The US has recommended an 80km exclusion zone.
Tepco vice president Norio Tsuzumi has visited evacuation centres to meet those forced from their homes.
Bowing deeply, he said: "Since I have tried to manage this problem hand-in-hand with the government, my visit here to directly meet you was belated. For this I also apologise from the bottom of my heart."
Meanwhile, strong aftershocks are continuing to rattle the north-east of Japan, adding to the misery of more than 300,000 people still huddled in evacuation centres across 16 prefectures.
Tens of thousands of homes are still without power and more than two million people have no running water, officials say.