The decision to remove emergency staff came as radiation levels spiked to their highest levels so far at Reactor 3 and a second fire broke out at Reactor 4.
Shortly after the evacuation, a military helicopter was seen carrying water to the plant, apparently to cool down the most troubled reactors, according to Japan's NHK public broadcaster.
Chief cabinet secretary Yukio Edano told reporters: "The workers cannot carry out even minimal work at the plant now."
The latest fire is believed to have started in the outer housing of the fourth reactor's containment vessel.


The flames were brought under control but white smoke or steam has been seen rising from the facility in the northeast of the earthquake and tsunami-devastated country.
Officials have been struggling to address the failure of safety systems at several of the plant's reactors.
There are six reactors at the plant, and the three that were operating at the time of the magnitude 9.0 earthquake and tsunami.