General Touka Ramadan Kore, the chief of army staff, said on Wednesday that his forces had halted a week-long offensive by the rebels, who he called "Sudanese mercenaries".
He also said that his soldiers had managed to recover about 40 military vehicles seized by the National Alliance during earlier clashes.
Chadian rebels launched their latest offensive against the government of Idriss Deby, the president, on June 11 by with a series of raids on towns in the east of the country.
Gueddei warned that the rebels were not defeated and could launch another assault on the capital Ndjamena, as they did in February.
"For the moment, we are regrouping our forces in the region of Am Zoer. Those who say it is over are wrong ... The objective remains Ndjamena. Wait a few days," he said.
Chadian officials frequently accuse the Sudanese government of backing the rebels, a claim that Khartoum dismisses.
Last month, Sudan broke diplomatic relations with Chad, accusing its neighbor of backing an attack near Khartoum by the Darfur-based Justice and Equality Movement .
Chad, in turn, closed its border with Sudan and halted bilateral trade.
On Thursday, Khartoum asked France to help ease the tensions with Ndjamena.
"Sudan is not at war with Chad. We are not going toward a war," Deng Alor, Sudanese foreign minister, said following talks with his French counterpart Bernard Kouchner in Paris.
"Because of the complexity of the situation, we are asking our friends, the French to help the two countries."