The attack yesterday hit a truck convoy transporting Muslims to Bouar, in the north-west of the country, leaving up to 50 people injured.
"It is a sign of the still fraught and highly dangerous situation in the Central African Republic that children and their families have been attacked and killed while trying to evacuate to safety," said Robert Lankenau from charity Save the Children in a statement.
He added that while peacekeeping troops from the African Union and France have been trying to restore stability in the country, "it's clear that this protection is not reaching children in more remote areas".
Sectarian violence has gripped the landlocked country after a March 2013 coup launched by the mostly Muslims Seleka rebels who installed their leader as president in the mainly Christian country.
Some of the Seleka turned rogue and carried out a string of atrocities including killings, rape and pillage, prompting Christians to form vigilante groups in response, and plunging the country into a vicious cycle of revenge attacks.