"The government informs the national and international communities that about 40 members of the Chadian army have deserted the ranks aboard three vehicles," a 14 October communique said.
The soldiers traveled to Hadjer Hadid, a town in the eastern Ouaddai region, the government said.
The statement continued, "The situation in eastern Chad is calm and under the control of the Chadian army."
Eastern Chad – which abuts Sudan's Darfur region – has been gripped with tension since the Darfur conflict broke more than two years ago. Hostilities have time and again spilled over into Chad, where nearly 200,000 Sudanese refugees are living in camps.
Chadian President Idriss Deby last year accused the Sudanese government of backing a 3,000-strong rebel force operating at the border.
Late last month Deby blamed the Sudanese militia known as the Janjawid for a cross-border attack in which at least 50 civilians were killed in the Ouaddai region.
The Darfur conflict and its spreading hostilities have proved a knotty situation for Deby, a former warlord who took power in a coup in 1990 then was elected in 1996 and 2001. He seized power with the backing of Sudan, but is of the same ethnic group as rebels fighting the Sudanese army and allied militias.
Deby has long faced tensions within the ranks of his armed forces. And diplomats say mutineers that staged an uprising in N'djamena last year are from Deby's Zagawa ethnic group and were expressing anger at their president's lack of support for his kinsmen being battered in Darfur.
In its communique, the government said the desertion incident was "contrary to reports by a certain press," without specifying an organisation. A Chadian opposition website, Alwihda, recently posted a story reporting that about 500 heavily armed "rebel" soldiers in 30 vehicles deserted and headed to the east.