President Ghani joined Afghan National Security soldiers in carrying the Nakamura's coffin draped in an Afghan flag to the awaiting aircraft.
Nakamuro's wife, Naoka and daughter, Akiko, had traveled to Afghanistan along with three of his colleagues, to accompany his body home to Japan.
Ghani called the death of Nakamura a big loss to the people of Afghanistan and promised that national police would search and arrest the killers. He called Nakamura, to whom he had earlier given honorary Afghan citizenship, a hero.
Nakamura's killing shocked many Afghans and candlelight vigils were held throughout the country. Giant posters emblazoned with his picture still adorn parts of the capital.
Hundreds of social media posts in Afghanistan expressed sorrow and outrage over the attack. One post carried a drawing of the Japanese physician, with the words: “Sorry we couldn’t save you Nakamura.”
Authorities in eastern Nagrahar province where the shooting occurred said they had received intelligence earlier that Nakamura may be targeted in an attack and had warned Nakamura to be particularly cautious. Nakamura was traveling with three guards when he was killed. His guards also died.