Two local CAR employees of the Agency for Technological Cooperation and Development, or ACTED, were killed Saturday as they returned to the organization's base in Bossangoa in northwest CAR.
"The Central African employees, one of which originating from the region, knew the area well and were clearly identified and identifiable as humanitarian workers when they were attacked," the organization said Sunday.
The rebel Seleka coalition toppled the government early this year. It's suspected of committing war crimes in the country, prompting the International Criminal Court to investigate the situation.
The United Nations said incidents of arbitrary arrests, torture and other acts of violence in the capital have uprooted thousands of people in recent weeks.
Kristalina Georgieva, the European Union's commissioner for crisis response, said the attack on aid workers was a human tragedy.
"It is beyond words and absolutely unacceptable to target people who are working to save the lives of others," she said in a statement Tuesday.
ACTED is a humanitarian partner organization of the EU. Georgieva said the humanitarian situation in CAR was "dramatic" and aid workers should be protected, not attacked.
"An already desperately destitute population is being pushed to the limit," she said. "This is clearly unacceptable."