Acting Defence Minister Emmanuel Nadingar said the latest raid took place on Sunday and was the third such attack from Sudan's western Darfur region in less than a week - despite a ceasefire agreement signed last month.
Chadian troops clashed at least twice with the Janjawid militia over the past few days and killed 60 of their fighters last Wednesday, according to Nadingar.
He also said Sudanese combat helicopters had flown over Chadian territory on Friday, where an estimated 100,000 Sudanese refugees have sought shelter.
"The Sudanese government must respect the accord and rein in the Janjawid, we consider this an aggression against our people and that gives us the right to protect our territory and our people."
In Khartoum, Sudan's minister of state for foreign affairs, Najib al-Khair Abd Al-Wahab, said the government would do all it could to avoid any escalation.
Chad has recently brokered a truce between Khartoum and two rebel groups to enable urgent food and medical supplies to reach hundreds of thousands of people forced from their homes by more than a year of violence in the impoverished Darfur region.
But fighting resumed last week, exacerbating a humanitarian and refugee crisis that has sparked international concern.
UN and human rights groups have accused the Sudanese government and the Janjawid militia of ethnic cleansing in Darfur and massive human rights violations which they say may constitute war crimes and crimes against humanity.
Chad National Army promises
more agressive response to raids
The African Union has sent a mission to the region - where two rebel groups took up arms in February last year demanding a fairer share of power and resources - to assess conditions for the deployment of ceasefire monitors.
The rebels accuse the Sudanese government of neglecting arid Darfur and arming militia to drive black Africans out of their villages, killing, looting and raping along the way.
Threat to agreement
Khartoum, which denies the accusations that its forces took part in massacres and summary executions, has branded the militia outlaws, but says they are beyond its control.
Under the 45-day, renewable truce agreement signed in Chad's capital Ndjamena, the warring factions were meant to reconvene soon to discuss a global peace deal for Darfur, but the latest violence has cast a shadow on any future talks.
"The latest events have put into question all the efforts that the president of the republic, the government and our country are making to restore peace at the border and in Sudan," Nadingar said.