President Francois Hollande meanwhile said his decision to deploy 1,600 troops in the former French colony was intended to prevent "crimes against humanity".
"France is worried by the dismissal of three ministers and the Treasury Director, announced by [interim president] Michel Djotodia, without the counter-signature of Prime Minister Nicolas Tiangaye," said Vincent Floreani, deputy spokesman at France’s Ministry of Foreign Affairs.
"This move, which contradicts the constitutional charter of the transition, is likely to further exacerbate instability," he warned.
Finance Minister Christophe Bremaidou, Security Minister Josue Binoua, Livestock Minister Joseph Bendounga and Treasury Director Nicolas Geoffroy Gourna-Douath were all dismissed under presidential decrees issued by Djotodia.
Djotodia, whose rebel coalition Séléka seized power in Central African Republic with the ouster of president Francois Bozizé in March, is heading an interim government which is due to step down by the end of next year.
Djotodia has repeatedly vowed to remain faithful to the principles of the January 2013 Libreville peace accords, which Seleka signed with the opposition and Bozizé's regime.
The country has descended into chaos since the March coup, with Muslims and Christians engaged in fierce clashes.
Some 600 people have been killed in the last 11 days and two French soldiers were killed last week. The French force is supporting an African mission trying to restore order.
Speaking in Paris at a ceremony on Monday to honour the two fallen soldiers, the French president said it was to France's credit that it had intervened in the Central African Republic but he added that the full French mission "will not stay for the long term" in the country.
The soldiers who were killed last week, Antoine Le Quinio who was 22, and 23-year-old Nicolas Vokaer, were both members of the crack Eighth Parachute regiment.
They were posthumously promoted to the rank of corporal and awarded the Légion d'Honneur, France’s highest award.
"When crimes against humanity are committed, it is an honour for France and her soldiers to take action to end them and to do this without the slightest hesitation," Hollande said.