The three were detained in March and had admitted their criminal actions, said the official Korean Central News Agency (KCNA) without explaining why one was deported.
"What they did is a very grave violation of the law of the DPRK (North Korea) and international law and they will, therefore, face proper legal actions," it said.
The three had entered the Rason free trade zone to work for Japanese firms, the agency said without giving further details of the charges.
The trio visited Rason to check machines at a food processing factory, Japan's Asahi Shimbun newspaper reported last month.
The paper said they were detained on charges that they hid drugs in canned goods to be exported to China.
KCNA named the two still in detention as Hidehiko Abe of Realise Co., and Takumi Hirooka of Sugita Industrial Co. It said Masaki Furuya, former representative managing director of JP Dairin Co., had been expelled.