Officials said on Tuesday that about 28,500 people had already left the alert zone - a large area of which was devastated by the tsunami.
But about 30,000 still remained, according to the government.
"We have hoped to let evacuees return to their ordinary lives as soon as possible. It took five months to finally start the process," said Goshi Hosono, the minister in charge of the nuclear crisis.
"We will carry this out very cautiously."
Although no-one has died as a result of the nuclear crisis, the meltdown at Fukushima has turned large section of the public against nuclear power.
Public concerns have been fuelled by a string of revelations about contaminated food products such as beef, leafy vegetables and milk.
On Tuesday, lobby group Greenpeace claimed it had tested fish caught in the sea 55km from the plant, and had detected higher levels of caesium than normal.
Prime Minister Naoto Kan, struggling to hold on to power amid collapsing popularity, has taken on the anti-nuclear cause and promised to reduce Japan's reliance on nuclear energy.
About 30% of Japan's electricity was nuclear generated before the Fukushima crisis.
But since the crisis, two-thirds of the country's reactors have remained closed as the government tries to stave off concerns over safety by carrying out stress tests.
Much of the country has instituted power saving measures such as rolling blackouts in a bid to save energy.
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