“I am not fooled by the justification that violence is necessary for the sake of democracy and modernization,” he wrote in an old posting on his website.
“True happiness for mankind should be realized not through violence or money, but in a humane way.”
Nakamura also described a variety of his organization’s projects to help Afghans, including the construction of wells and irrigation canals, as well as health services.
Jalalabad resident Auzubillah, who only uses one name, told AFP that he heard shooting at about 8:00 am (0330 GMT).
“I saw there were gunmen attacking a Japanese and his security guards,” he said. “Then the gunmen left the area through a small street.”
Photos from the scene showed a white pickup truck with a large cabin. Its side windows appeared to have been shot out, and at least three bullet holes could be seen in the windscreen.
The Taliban denied responsibility for the attack, saying they have “good relations” with organisations that “contributed to the reconstruction of Afghanistan”.
Nangarhar was once a hotbed of activity for the Islamic State group’s Afghanistan affiliate.
Authorities recently claimed the jihadists have been territorially defeated in the province — but small cells are thought to remain.
Aid agencies and non-governmental groups are sometimes targeted in Afghanistan’s war.
The Taliban in May struck Counterpart International, a US-funded non-profit group working with marginalised people. Nine people were killed in that attack.