President Michel Djotodia, who is the former leader of the Seleka rebel coalition, announced the dismissal of Jean-Pierre Dolle-Waya in a statement on Tuesday.
The statement said Waya would be replaced by a former national security director, General Ferdinand Bombayake.
“The change at the head of the army today is linked to the current situation in the country’s north and the president’s desire to bring some corrections in the security sphere,” Djotodia’s spokesman Guy Simplice Kodegue said.
In the clashes that took place in the town of Bossangoa, in the northwest, between Saturday and Monday, an estimated 100 people were killed, the spokesman said.
Kodegue added that around 30 houses had been burned and two bridges destroyed, cutting off the region from the capital Bangui.
The fighting occurred between the supporters of ousted President Francois Bozizé and Seleka fighters loyal to the new president.
The initial death toll announced by the government stood at 60.
Levy Yakete, a spokesman for Bozizé, said the attacks were carried out by former army men who are attempting to bring Bozizé back to power.
“We have a collection of free officers of (former) armed forces who lead the operations,” he said.
The Seleka rebels launched an offensive against the CAR government in December 2012.
On January 11, then President Bozizé and the representatives of the Seleka rebels signed an agreement in Libreville, Gabon, after three days of negotiations brokered by regional neighbors.
However, the deal fell through, and Djotodia, leading thousands of Seleka rebels, captured Bangui and proclaimed himself president after seizing power from Bozizé on March 24.
There are many mineral resources, including gold and diamond, in the Central African Republic. However, the country is extremely poor and has faced a series of rebellions and coups since it gained independence in 1960.