Chad's defence minister, Bichara Issa Djadallah, accused Sudan of allowing the deserters to collude with armed Chadian rebels whom he said the Sudanese authorities had long been harbouring within Darfur.
"We deplore the fact that under the benevolent eyes of the local authorities in Darfur, they have formed an alliance with the armed (Chadian) opposition installed in Darfur and long supported by the Sudanese authorities," Djadallah said.
"Given this situation, the Chadian government reserves the right to pursue them," he said in an address on state radio late on Tuesday.
The dissident soldiers have said they number around 600 men and call themselves the Platform for Change, National Unity and Democracy, whose French acronym is "SCUD". They are demanding Deby step down and that he free political prisoners.
Djadallah said he believed the group was made up of 86 men, higher than earlier government estimates.
Deby has created a new elite security force charged with ensuring his safety days after dissolving his Republican Guard, a move analysts and diplomats said was aimed at instilling order in the military and ensuring the survival of his administration.