The attack was carried out around 8 am in Jalalabad of eastern Nangarhar province when, Tetsu Nakamura, a physician and the head of Peace and Medical Service (PMS) charity, was driving through the city area, provincial governor's spokesperson Attaullah Khogyanai told EFE.
"Unfortunately, doctor Nakamura lost his life due to his injuries (sustained in the attack)," Khogyanai wrote on his Twitter handle.
Earlier, the spokesperson said Nakamura, who was known for helping with rebuilding efforts in war-torn Afghanistan, was wounded while five people lost their lives in the attack.
Among the dead are three of Nakamura's bodyguards and a driver of the aid agency, the spokesperson said. The identity of the sixth victim was not known.
President Ashraf Ghani's spokesperson Sediq Sediqqi said the government "strongly condemns the heinous and cowardice attack on Afghan's greatest friend, Dr. Nakmura".
Seddiqi paid tributes to the slain aid worker "who had dedicated all his life to change the lives of Afghans, working on water management, dams and improving traditional agriculture in Afghanistan".
Nakamura served as Executive Director of the charity in Afghanistan since 2008. The nonprofit assists in agriculture and irrigation projects in Nangarhar.
He was given the Ramon Magsaysay Award, widely recognized as "Asia's Nobel Prize", in 2003. The award was in recognition for his years of work in providing food and medical services to Afghan refugees in Pakistan before he moved to Afghanistan.
"Nakamura and his organization have served people in Nangarhar for years. Not only Nangarhar official, but all people are deeply saddened because of this attack," Nangarhar Governor Shah Mahmoud Myakhail said in a statement.
The governor said efforts were on to evacuate him to Kabul for specialized treatment.
No group immediately claimed responsibility for the attack in the province where both Taliban and Islamic State militant groups are active.
Taliban spokesperson Zabihullah Mujahid said the insurgent group "has nothing to do with" the attack on the Japanese aid agency.
"The charity enjoys good relations with the Islamic Emirate and none of them is a target for the mujahideen of the Islamic Emirate," Mujahid wrote on Twitter.
Nangarhar police spokesman Sayed Khan told EFE that the area where the attack took place had been cordoned off and a manhunt launched to nab the assailants.
The attack comes days after a United Nations worker was killed when a hand grenade was launched at a vehicle in Kabul city on November 24.
The deceased was a foreign national who worked for the United Nations Assistance Mission in Afghanistan.
Five civil, including two Afghan employees of the UNAMA, were also wounded in the blast in Afghanistan's capital.
( With inputs from IANS )