Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX. 3 O2 + protoporphyrinogen IX = 3 H2O2 + protoporphyrin IX Binds 1 FAD per subunit. Inhibited by acifluorfen. Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; protoporphyrin-IX from protoporphyrinogen-IX: step 1/1. Porphyrin-containing compound metabolism; chlorophyll biosynthesis. Expressed at high levels in the leaves and at low levels in the roots and floral buds. Belongs to the protoporphyrinogen/coproporphyrinogen oxidase family. Protoporphyrinogen oxidase subfamily.