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Wakata, 50, had been a space station flight engineer since he and two crewmates arrived on Nov. 7.
"I am humbled to assume the command of the space station," Wakata said during a change-of-command ceremony broadcast on NASA Television.
Outgoing station commander Oleg Kotov, flight engineer Sergey Ryazanskiy, both from Russia, and NASA astronaut Mike Hopkins are due to depart the orbital outpost on Monday. Their replacements arrive on March 26.
Wakata's command marks just the third time the station is being overseen by a crewmember who is not from NASA or the Russian Space Agency, the two primary partners of the 15-nation project.
Canadian Chris Hadfield served as commander from March to May 2013. European Space Agency astronaut Frank DeWinne led a station crew in 2009.
"I am very proud as a Japanese to be given this important command," Wakata, speaking Japanese, said through a translator.
"I think that this reflects the real trust toward Japan and what Japan has achieved over the past years," he said.
So far, four Japanese astronauts have served as space station crewmembers, including Wakata, who previously flew in 2009. Wakata also is a veteran of two space shuttle missions.
Along with NASA astronaut Rick Mastracchio and Russian cosmonaut Mikhail Tyurin, Wakata is scheduled to remain aboard the station until mid-May.
One of his first tasks as commander will be to oversee the arrival of a Space Exploration Technologies' Dragon cargo ship which is due to launch from Cape Canaveral Air Force Station in Florida next Sunday and reach the station on March 18.
The station, a $100 billion research laboratory, flies about 260 miles (about 420 km) above Earth. It has been permanently staffed by rotating crews of astronauts and cosmonauts since November 2000.