"They were arrested late on Tuesday evening after they refused to go back to Chad," said Hassan Barghu, responsible for west and central African affairs in Sudan's ruling National Congress party.
Chadian Defence Minister Bichara Issa Djadallah earlier this week accused Sudan of allowing scores of army deserters to collude with Chadian rebels whom he said the Sudanese authorities had long been harbouring within Darfur.
Barghu declined to comment on the defence minister's warning that Chad was ready to pursue the deserters inside Darfur.
"We have not heard anything to that effect from the Chadian authorities," Barghu said. "We are in daily contact with the Chadian government."
He said the soldiers, including two senior officers, were arrested in the town of el-Geneina near the Chadian border. "We will send them to the International Committee of the Red Cross."
Chad's government said it was surprised at the reports and had not been officially informed. It cast doubt on the number of soldiers involved, saying that as far as it knew, only two deserters had been arrested in Sudan.
"It concerns one vehicle with two soldiers on board, seized by the Sudanese authorities, who only returned the vehicle to Chad but kept the soldiers and their arms," a communique signed by Chad's Communication Minister Hourmadji Moussa Doumgor said.
The dissident Chadian soldiers have said they number around 600 men and call themselves the Platform for Change, National Unity and Democracy. They are demanding Deby step down and that he free political prisoners.
Djadallah has said he believed the group was made up of 86 men and that they were 100 km (62 miles) over the border, north of el-Geneina.
Barghu said the Sudanese authorities had no information about how many more Chadian deserters were in Darfur, where mainly non-Arab rebels launched an uprising in early 2003 accusing Sudan's government of monopolising wealth and power.
Sudan and Chad have set up joint border patrols during the revolt in Darfur, which spilled over into Chad as more than 200,000 Darfuris crossed the border to flee the fighting.
Tens of thousands of people have been killed and more than 2 million forced from their homes during the violence in Darfur.
Deby, himself a former army chief who seized power in Chad in 1990, has been credited with bringing a measure of stability to Africa's newest oil producer, although he has long had a tense relationship with the military.
He has dissolved his Republican Guard and created a new elite security force charged with ensuring his safety in a move analysts and diplomats said was aimed at instilling order in the military and ensuring the survival of his administration.