Chad’s Communications Minister Hourmadji Moussa Doumgor said that "a coup attempt was foiled between the afternoon of Tuesday March 14 and today" when Mr Deby had been due home from a summit in Equatorial Guinea.
The "masterminds" of the plot were allegedly the twins Tom and Timane Erdimi, nephews of Mr Deby and former chiefs of his civilian personal staff.
They joined the exiled opposition in December, and renegade former general Seby Aguid, who defected to a rebel movement in February.
An investigation is underway to track down all those involved and determine their roles in the coup bid.
According to Mr Doumgor the army had been tipped off about the coup attempt and security forces were out in strength on Wednesday morning in the capital Ndjamena.
Mobile phone links were cut, but nobody reported any gunfire during the night.
"Those who escaped fled in seven vehicles, of which two were intercepted and the occupants neutralised," Mr Doumgor said, without being specific about their fate.
The aim of the plotters was to detabilise the regime, then assassinate Mr Deby by shooting down his plane when he returned from a six-nation summit of the Central African Economic and Monetary Community (CEMAC), according to the government.
However when he was told of the plot, Mr Deby cut short his trip to Equatorial Guinea and returned to Ndjamena on Tuesday) night and to personally take charge and restore order.
Mr Deby, a former guerrilla leader, himself first came to power in a coup in December 1990. Six years later he won the sub-Saharan nation's first multi-party presidential election since independence from France in 1960.
He faces a rebel insurgency mounted by a movement in the east on the border with Sudan, the region from which he launched his power grab. His rebel foes include military men mainly from his own ethnic group, the Zaghawa.
They have formed a Foundation for Change, National Unity and Democracy (SCUD) to overthrow him.