Shinzo Abe also said he stood by assertions he made at a meeting of Olympic chiefs that the effect of contaminated water was contained.
Those reassurances, given at a meeting of the International Olympic Committee in Buenos Aires, were seen as key to Tokyo's successful bid to host the 2020 Olympic Games.
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Today's visit came as it emerged that just months after the March 2011 disaster, authorities allowed operator Tokyo Electric Power (TEPCO) to shelve costly plans to deal with groundwater over fears it would push the massive utility into bankruptcy.
Hundreds of tonnes of groundwater are becoming contaminated daily as they mix with highly polluted water used to cool the broken reactors. The water then flows out to sea.
Abe wore a full face mask and an orange helmet for the tour, along with a white Tyvek protective suit that had the words "Prime Minister Shinzo Abe" emblazoned on the back in black. He was escorted around the site by TEPCO executives, including president Naomi Hirose.
The visit is part of a campaign aimed at reassuring the world about the state of the plant, more than two-and-a-half years after it was battered by a huge tsunami.
Speaking to Olympic chiefs in Buenos Aires just ahead of a decision to award the Games to Tokyo, Abe said of the plant: "Let me assure you, the situation is under control."
But some critics and experts say Abe's gloss on the disaster is bordering on the dishonest -- a senior TEPCO executive flatly contradicted the PM earlier this month.
"I think the current situation is that it is not under control," he told opposition lawmakers.
TEPCO has poured thousands of tonnes of water onto the Fukushima reactors to tame meltdowns sparked by the March 2011 earthquake and tsunami.
The utility says they are now stable but need more water every day to keep them cool and to prevent them running out of control again.
Much of that now-contaminated water is being stored in temporary tanks at the plant, and TEPCO has so far revealed no clear plan for its disposal.
The problem has been worsened by leaks from some of those tanks that are believed to have seeped into groundwater or begun to make their way out to sea.