Tetsu Nakamura's body will be returned home to Japan.
"Today is a day of grief and sadness. Dr. Nakamura was a great personality, who dedicated his whole life for the prosperity of the Afghan nation and the most deprived people and reconstruction of this country," President Ashraf Ghani said in a speech at Kabul airport on Saturday, Efe news reported.
Ghani attended the ceremony and carried Nakamura's coffin on his shoulder in tribute to the slain aid worker, who had been head of the Peace and Media Services (PMS), a Japanese charity organization.
"On behalf of the Afghan nation, I express my sympathies to his family, to the whole nation of Japan and Japanese prime minister," the Afghan president said while standing near the coffin.
An Afghan national flag was draped over his coffin and Ghani called him an "Afghan (national) of Japanese origin" as well as "the hero of Afghanistan."
Nakamura was given Afghan citizenship by Ghani in recognition of his services to agriculture and water management in the east of the Asian country throughout the year.
Ghani said Nakamura helped "hundreds of thousands" of poor people to find a livelihood and got "hundreds of thousands" of trees planted and grown after controlling parts of the Kunar river in order to irrigate desert and turn it into land for farming.
Nakamura's wife and daughter attended the ceremony.
Ghani promised his government would bring the culprits of the attack on Nakamura to justice.
"Afghanistan's brave army, police and intelligence will identify these traitors and will be bringing them to justice," he said.
The aid worker, who had served in Afghanistan for nearly three decades, had for the past eight years been working as the head of PMS.
He was killed Tuesday by unknown armed men in Jalalabad city, eastern Nangarhar province, along with his five others - his driver, three bodyguards and another colleague.
No group has claimed responsibility for the attack.
( With inputs from IANS )