They arrived at Narita International Airport, in Chiba Prefecture, and are scheduled to fly to Fukuoka from Tokyo’s Haneda airport on Monday morning.
Before they left Afghanistan on Saturday, the Afghan government held a ceremony at an airport in Kabul, with President Ashraf Ghani joining soldiers to carry Nakamura’s coffin wrapped by the country’s flag toward a plane.
The 73-year-old Nakamura, who headed the Peshawar-kai aid group based in the city of Fukuoka, and five Afghans including his driver were killed Wednesday as armed men attacked their vehicle in Jalalabad, in the eastern province of Nangarhar.
His wife and eldest daughter arrived in the Afghan capital Friday and met with Ghani.
Authorities in the province have said they obtained information about a possible attack against Nakamura about a year ago but could not prevent the five from being killed, adding they had sent four bodyguards to protect him.
They also said they warned Nakamura the day before the attack that danger was increasing.
Armed anti-government groups, including the Taliban and the Islamic State, operate in the province. But Gov. Shah Mahmood Miakhel told local reporters Thursday there is evidence that the attack was planned outside of Afghanistan. However, he provided no details, saying more investigation is necessary.