Foreign Secretary Alberto del Rosario said the priority would be Filipinos who live within 50 kilometers (31 miles) from the Fukushima plant, for which the evacuation was "mandatory" - although he admitted that the government can not force residents to leave.
Cheap at home will also be offered to those within a radius of 100 kilometers of the plant, he said.
"We're going to move as fast as we can for those in areas where the risk is greater," he told a press conference announcing Manila chartered aircraft would be available for an estimated 2,000 Filipinos April 17 .
Health authorities will display on arrival in Manila for any disease that could be related to nuclear disaster, he added.
The Philippine government later released figures saying more than 3,000 Filipinos living within 100 kilometers of the plant.
Del Rosario admitted Manila could not compel any Filipinos in Japan to leave against their will, adding that many of its citizens in the affected areas are married to Japanese nationals and not wishing to be repatriated.
Japan upgraded its nuclear emergency months to a maximum of seven on an international scale of nuclear crisis on Tuesday, placing it on par with the Chernobyl disaster a quarter of a century.
Tokyo is preparing to evacuate more people living near the plant, which stretches 20 kilometers (12 mile) exclusion zone to other cities.
Previously, a small number of Filipinos were taken back home by the government after having been displaced by the massive March 11 earthquake and tsunami.
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