The NGO vehicle came under fire in Jalalabad city on Wednesday morning, leaving the doctor injured and his driver and security personnel killed, according to Afghanistan's Tolo News.
Japan's NHK reported later in the day that the doctor succumbed to his wounds in the hospital.
Nobody has taken responsibility for the attack so far.
The Afghan government has been engaged in a vicious struggle with the Taliban movement for almost two decades. The conflict-stricken country continues to serve as a breeding ground for various insurgent and militant groups affiliated with al-Qaeda and the Islamic State terrorist organisation.
*Daesh (also known as ISIS/ISIL/IS) and al-Qaeda are terrorist groups banned in Russia