This invention describes a method which permits direct treatment of natural cork stoppers, using supercritical fluids with the aim to eliminate or significantly reduce the quantity of cork contaminants, namely 2, 4, 6-trichloroanisole. The process uses a separating device which permits natural cork stoppers to go through compression/decompression cycles without losing their shape and maintaining their sealing properties. This invention refers also to the natural cork stoppers treated by this method.