Addressing the media, Justice Minister Masako Mori announced the execution of Wei Wei, a Chinese national aged 40, reports Efe news.
His death sentence was handed out in 2005 but finalized after appeal on November 10, 2011 for the murders carried out in June 2003 in Fukuoka city.
The four victims, members of the same family including two children, were allegedly killed by being thrown in the sea tied to weights.
The execution was ordered by Mori on Monday and carried out on Thursday in Fukuoka.
In the press conference, Mori called Wei's case "extremely savage and cruel", recalling that the victims included a boy aged 11 and a girl aged eight, along with their parents.
Wei Wei was the first person to be executed in Japan since August 2, also marking the 39th execution during the uninterrupted reign of Prime Minister Shinzo Abe since 2012.
On August 2, two inmates, who were sentenced to death over separate charges of the rape and murder of women, were hanged.
A total of 15 death-row inmates were executed in 2018, including Shoko Asahara, the founder of the Aum Shinrikyo doomsday cult that carried out a deadly Sarin gas attack on the Tokyo subway in 1995.
Another 12 members of the cult were also executed, and in December 2018, two death-row inmates who were convicted over the murder of a company president and one of the firm's employees in 1988 were hanged.
Japan is the only industrialized and democratic nation apart from the US that carries out capital punishment, and death-row inmates are kept in solitary confinement and informed about their execution just hours before they are hanged.
It currently has 112 convicts on death row.
( With inputs from IANS )