A heavily armed rebel group had launched a raid from its rear base in Libya on April 11, the same day as Chad's presidential election that is expected to see incumbent Idriss Deby Itno returned to power.
The raid by the Front for Change and Concord in Chad (FACT) has since resulted in "more than 300 rebels neutralized" and claimed the lives of five government troops, army spokesman General Azem Bermandoa Agouna told AFP.
Bermandoa said 36 soldiers had been wounded in fighting on Saturday and 150 rebels taken prisoner, including three senior members.
The government has said that the rebel offensive in the provinces of Tibesti and Kanem was over.
FACT, for its part, said in a statement on Sunday that it had "liberated" the Kanem region that saw clashes on Saturday.
The Tibesti mountains near the Libyan frontier frequently see fighting between rebels and the army, as well as in the northeast bordering Sudan.