In a simple ceremony onboard the station, Wakata took over the facility's command from Russian predecessor Oleg Kotov, the Japan Aerospace Exploration Agency said late yesterday.
Most previous ISS commanders have hailed from Russia or the United States.
"I am humbled to be assuming command of the station," Wakata said in a video, as he thanked fellow astronauts who were returning to Earth.
"We have had unforgettable memories together."
Wakata, 50, a veteran of several space missions, left for the ISS in November on Russia's Soyuz rocket, and will serve as the commander until May when he is scheduled to return home.
Kirobo, a pint-sized android equipped with artificial intelligence, was sent as part of a longer-term project to see how a robot can act as a companion for isolated people, particularly to see if it can develop conversational skills.