Allam-Mi told Reuters: "The Sudanese air force began yesterday to fly over the positions of the Chadian army. I summoned the Sudanese ambassador in Chad this morning to raise a strong protest and I said that Chad would take all the necessary measures."
Chad also accused Khartoum of supporting rebels who are fighting a low intensity war in eastern Chad to oust Idriss Deby, the Chadian president.
Sudan has, however, denied the claims and said that troops from Chad had in fact crossed into Sudan.
But the Chadian minister rejected Sudan's accusations, calling them propaganda. Allam-Mi said: "This is a pretext to continue to attack our country.
Sudan is reassembling and rearming its mercenaries, as the attack against Ounianga Kebir demonstrates."
The anti-Deby rebel Union of Forces for Democracy and Development (UFDD) occupied the remote northeastern town of Ounianga Kebir early on Saturday morning.
Violence in the east of oil-producing Chad has been fuelled by instability and ethnic killings spreading across the border from the neighbouring Darfur region of Sudan.
The latest foray by the rebels appeared to be a hit-and-run raid typical of their long-running insurgency.
A rebellion and related conflict in Darfur has killed some 200,000 people since 2003.
Deby, a former fighter pilot, seized power in a 1990 uprising in eastern Chad and was re-elected to a fresh term in May in elections boycotted by the opposition.