Mujahed said the group was lost and the victims were killed as they tried to escape.
Dirk Frans, the director of the the International Assistance Mission charity, told The Associated Press news that the group was returning to Kabul from an eye facility in Nuristan province when they were killed.
"This tragedy negatively impacts our ability to continue serving the Afghan people as IAM has been doing since 1966," a statement released by the nonprofit Christian organisation which provides healthcare services said.
"We hope it will not stop our work that benefits over a quarter of a million Afghans each year."
IAM says it provides the majority of eye care available to Afghans, running eye hospitals in Kabul, Herat, Mazar and Kandahar.
Al Jazeera's James Bays, reporting from Kabul, said the area where the bodies were found was not considered one of the more dangerous places in Afghanistan, and that some of the workers had extensive experience with the country and its languages.
That means the killings are even likelier to make many of the non-govermental organisation working in the country reassess their operations, Bays said.
"I am sure it will limit some operations that have been benefitting the people of Afghanistan," he said.
General Agha Noor Kemtuz, the provincial police chief, said a third Afghan man, who had been travelling with the group, survived.
"He told me he was shouting and reciting the holy Quran and saying 'I am Muslim. Don't kill me'," Kemtuz said.
Kemtuz said the survivor told him that the group, which had been travelling in Panjshir, Nuristan and Badakhshan provinces, were surrounded by armed men and then attacked.
He speculated that robbery could have been a motive in the killings in the remote Kuran Wa Munjan district.
"We couldn't find any passports or anything," he said. "Nothing was left behind."
It was unclear what the group had been doing in the forested area away from main routes through the province.
"Before their travel we warned them not to tour near jungles in Nuristan but they said they were doctors and no one was going to hurt them," Kemtuz said.