JAEA announced that the men were exposed to radioactive sodium, iodine and more exotic elements Thursday at JAEA's Japan Proton Accelerator Research Complex Hadron Experimental Facility in Tokai, Ibaraki Prefecture.
An additional six workers are to be tested for radiation exposure, with 19 other J-PARC personnel escaping exposure.
The accident occurred around noon last Thursday but the JAEA didn't report it to the nuclear regulatory authorities until Friday night, The Japan Times reported.
The JAEA said the next day that that it initially believed that the radiation leak was minor and had been confined to the laboratory after radiation alarms went off.
In an apparently botched safety procedure, workers subsequently switched on the laboratory's ventilation system, expelling the radioactive contaminants out of the building into the local environment.
The contamination resulted from an experiment conducted by the High Energy Accelerator Research Organization, which was designed to generate subatomic particles by firing a proton beam at a gold-covered object.