His death sentence was finalized in 2011.
Japanese Justice Minister Masako Mori said Wei Wei, 40, was hanged for the slayings of clothing dealer Shinjiro Matsumoto, 41, his wife, Chika, 40, their son, Kai, 11, and daughter, Hina, 8, on June 20, 2003, in Fukuoka Prefecture. His wife and two children were found drowned, strangled and smothered.
Wei Wei, a 40-year-old Chinese national, was at a detention center in Fukuoka on Thursday, after being on death row for more than 16 years, Justice Minister Masako Mori said.
After killing the family, Wei and his two accomplices then weighted and handcuffed the bodies and dumped them into Hakata Bay, Mori, said at a news conference.
Japan now has 112 people on death row, including 84 seeking retrials, according to the justice ministry.
Justice Minister Masako Mori said at a news conference Thursday that she signed the execution order after careful examination, taking into consideration the global anti-execution movement.
Japan has more than 100 prisoners on death row and 15 were executed past year, including 13 members of the Aum Shinrikyo doomsday cult, the BBC reported. Since 2007, Japan has begun disclosing the names of those executed and some details of their crimes, but disclosures are still limited.
A Chinese man was hanged for killing three Chinese that he lived with near Tokyo and for injuring three, the Asahi Shimbun said.
The execution is the second this year after Japan hanged 2 men convicted of murder in August.
A 2014 government survey of around 1,800 people showed 80 percent thought capital punishment was "unavoidable", with only one in 10 in favour of abolishing it.
Today's execution brings the total number of executions since Shinzo Abe became Prime Minister in 2012 to 39. Fifteen were executed previous year, including 13 members of the Aum Shinrikyo doomsday cult.