Officials told RFE/RL on December 4 that gunmen opened fire at a auto carrying Tetsu Nakamura, a 73-year-old physician who headed a Japanese charity focused on improving irrigation and agriculture in Afghanistan, in the provincial capital, Jalalabad.
Tetsu Nakamura, 73, who headed Peace Japan Medical Services - known as Peshawar Kai in Japanese - was shot by gunmen while in a vehicle in Jalalabad in Nangarhar province.
The Dutch ambassador in Kabul, Ernst Noorman, called the killing "senseless", saying Dr Nakamura had dedicated his life to the "peace and development of Afghanistan".
The attack comes after a grenade attack on a United Nations vehicle in Kabul last month killed an American working for the United Nations and wounded five Afghans.
A senior Japanese Foreign Ministry official said information about the incident and Nakamura's death were provided by the local provincial government to the Japanese embassy.
Mitsuji Fukumoto, an official with Nakamura's organization, told reporters in Tokyo it had "no idea what was the reason behind the attack, whether it was a simple robbery, or whether it was conflict of interest".
Nakamura had worked in the region since 1984, initially providing aid in Peshawar, in north-west Pakistan, before opening a clinic in Afghanistan in 1991.
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"True happiness for mankind should be realised not through violence or money, but in a humane way".
He also said, "There is no way" that the aid group will abandon the irrigation improvement project in Afghanistan to which Nakamura had long devoted himself to fight malnutrition, a problem he found to be the root cause of illness in the region.
Jalalabad resident Auzubillah, who only uses one name, told AFP that he heard shooting at about 8:00 am (0330 GMT). "Then the gunmen left the area through a small street".
Photos from the scene showed a white pickup truck with at least three bullet holes in its windscreen.
No one immediately claimed responsibility for the attack, the second in as many weeks targeting aid workers in Afghanistan.
Zabihullah Mujahid tweeted that the insurgent group "has no connection" to Wednesday's attack and does not consider the Japanese charity a target in the holy war the Taliban are waging to create an Islamic emirate.
Also in the capital, the Taliban in May targeted Counterpart International, a US-funded non-profit group working with marginalised people. The Japanese doctor was among six gunned down in an attack Wednesday in the eastern Afghan city of Jalalabad.