The news comes after series creator Shigeru Miyamoto told a Spanish newspaper that he was concentrating his efforts on the sequel to the Gamecube originals.
"In a recent interview, Mr Miyamoto confirmed that a new Pikmin game will be shown at the E3 Expo in June," a Nintendo spokesperson told Eurogamer.
"He believes that anyone who has played Pikmin games in the past will enjoy playing."
During the same interview, Miyamoto also revealed plans to showcase Super Mario Wii U at this year's E3 event in Los Angeles.
Nintendo has since confirmed that the game is based on the four-player tech-demo on show at last year's event.
Nintendo recently registered a website domain for Super Mario 4. It is unclear whether this has anything to do with the Wii U game, or the planned 3DS offering.
Watch the Nintendo Wii U concept trailer below: