Humanitarian groups, too, expressed doubt about the claim on Saturday.
"The Sudanese air force targeted the Chadian villages of Bahai, Tine, Karyari and Bamina," Hourmadji Moussa Doumgor, the communications minister, said in a statement.
Doumgor said his government "expects the African Union, Cen-Sad [states in the Sahel-Sahara region] and the United Nations to condemn these bombings against peaceful Chadian citizens and to work to bring an end to these repeated attacks on Chad".
Doumgor, who is also government spokesman, said: "In the face of this new escalation of Sudanese aggression, all arrangements have been made to enable our defence and security forces to fulfil their responsibilities."
He gave no details of any casualties.
In Khartoum, Ali al-Saddek, the foreign ministry spokesman, denied the claims.
"These accusations are without basis," he said. "We do not have air forces in that part of Sudan close to these locations and no intention of any escalation with Chad.
"We are astonished that Chad would resort to such accusations at the moment," he said.
A humanitarian organisation source in N'Djamena said that their team on the ground could not confirm the bombings announced by the minister.
Another non-governmental organisation said: "Our colleagues in the region saw nothing; this news seems to me rather surprising. We are not in Tine but we have a team in Bahai."
The Chadian government has accused Sudan of aiding rebels who are seeking to overthrow Idriss Deby Itno, the president.
"We are astonished that Chad would resort to such accusations at the moment"
Ali al-Saddek, Sudan's foreign ministry spokesman
For its part, Sudan accuses Chad of providing refuge to rebels from Darfur.
Also on Saturday, a Chadian rebel leader claimed that the fighting early in the week killed almost 80 people, with government forces accounting for 73 of the dead.
"We also took 43 prisoners and destroyed and seized numerous vehicles," said General Mahamat Nouri, head of the Union of Forces for Democracy and Development (UFDD).
The Chadian government said the fighting in the towns of Am Timan and Goz Beida left around 40 people dead, of whom 30 were rebels.
The army reclaimed control over the region without incident on Wednesday, with rebel forces retreating to far eastern Chad. Sudan denied any involvement in those attacks.