'Act of war'
Ahmed on Friday said that that there had been casualties in the first two alleged raids, calling them an "act of war".
Ahmed declined to comment on whether Sudan planned to retaliate, saying: "We are considering all options."
Mohammed Vall, Al Jazeera's correspondent in Khartoum, said the Sudanese government has consulted ambassadors of the permanent members of the UN Security Council, complaining of Chad's behaviour.
"There has never been an open war between the two countries, but this is a very serious development," he said.
"The Sudanese authorities have made it very clear that they reserve the right to retaliate."
Chad late on Friday hit back at Sudanese accusations saying Khartoum was "the robber who cries thief".
Mahamat Hissene, a government spokesman, told reporters that Chad "is surprised to learn that the regime in Khartoum is protesting against action by the Chadian air force on Sudanese territory".
Hissene said that any confrontations would be "simply the consequence of the attack on Chad organised by Sudan, using mercenaries armed, trained, financed and directed by satellite by the Khartoum regime".
Both countries have regularly accused each other of backing fighters bent on overthrowing their respective governments.
Ahmed said Sudan's foreign ministry had called in Chad's ambassador to demand an explanation for the two sorties and had informed the Khartoum-based ambassadors of the five permanent members of the UN Security Council.
Chad accused Sudan of backing an armed incursion into its territory last week, after the two countries had signed a pact in Doha, Qatar.
They had agreed in that deal to normalise relations and reject any support for rebel groups hostile to either of them.
Chad said it had stopped the advance, after clashes that killed 125 fighters.
Sudan denied involvement in the raid, saying it was a confrontation between Chad's government and "opposition groups".
Chad and Sudan resumed shaky diplomatic ties in November after cutting them in May 2008.
Sudan has accused Idriss Deby, the president of Chad, of being involved in an attack on the Sudanese capital by Darfur rebels on May 11, 2008.