Armed men stopped the "well-identified MSF convoy" and forced staff members and patients out of the cars and on to the ground before robbing them and killing one of the drivers, the group said in a statement yesterday.
The incident took place on Wednesday in Kouki, some 400 kilometres (250 miles) north of the capital Bangu.
"It is absolutely unacceptable that a team of medical workers and their patients were attacked while returning from providing lifesaving medical care," said Michelle Chouinard, MSF head of mission in CAR.
The charity said it was halting its activities in the area "until it receives adequate guarantees for the safety of its staff and the acceptance of its medical and humanitarian activities".
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MSF added that it expected "a full inquiry" by police and local authorities into the violence.
Doctors Without Borders, known by its French initials MSF, currently runs 17 projects across the Central African Republic.
The bloodletting in one of the world's poorest nations was so serious it triggered a military intervention by former colonial power France and led to the deployment of a UN peacekeeping force.
A peaceful presidential vote held in February was hailed as an important step towards reconciliation in the strife-torn nation.