On Wednesday, José Binoua announced the disarmament plan at a ceremony attended by President Michel Djotodia at the police headquarters in the capital Bangui.
Binoua said that Seleka fighters and civilians who possess weapons outside authorized security installations would be targeted by the program.
“No citizen of this country, or foreigner living in this country, can possess arms without the proper authorization from the Ministry of Territorial Administration,” Binoua said.
The program, which is expected to last at least 10 days, will require closure of boundaries of the capital, meaning vehicles will not be allowed to travel to and from the provinces.
Binoua called on the Seleka fighters to deliver any unauthorized weapons and warned of severe punishment in case of violation of the new regulations.
In July, a separate disarmament program was initiated by a regional peacekeeping force, which has not been effective enough since the force has had little presence outside the capital.
The Seleka rebels launched an offensive against the CAR government in December 2012.
On January 11, then President Francois 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 Michel 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.