Sudan denied that its planes had attacked the villages, and humanitarian groups in the region also expressed doubt about the Chadian claim.
"The Sudanese air force targeted the Chadian villages of Bahai, Tine, Karyari and Bamina, destroying the homes of peaceful Chadian citizens," Communications Minister Hourmadji Moussa Doumgor said, without giving details of casualties.
In a later statement, Foreign Minister Ahmat Allami told reporters that if Sudan did not halt its "aggressions", his country would strike back and "chase the Sudanese aggressors right back into their most remote bases in Sudan."
In Khartoum, foreign ministry spokesman Ali al-Saddek denied the Chadian claims.
"These accusations are without basis," he said. "We do not have air forces in the 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 added.
And a humanitarian organisation source in N'Djamena told AFP that "our teams present on the ground cannot at the moment confirm the bombings announced by the ... minister. Another non-governmental organisation source 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 President Idriss Deby Itno, and who resumed hostilities last on Sunday with an attack on a Chadian town near the borders with Sudan and the Central African Republic.
For its part, Sudan accuses Chad of providing refuge to rebels from Darfur.
Also on Saturday a Chadian rebel leader claimed 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), in a telephone interview with AFP. 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.
On Saturday's reported bombing raids, the communications minister said his government "expects the African Union... and the United Nations to condemn these bombings against peaceful Chadian citizens."
Chad and Sudan officially agreed to normalise relations on August 8, after months of hostility and accusations of supporting each other's rebel movements.
Sudan accuses Chad of interfering in Darfur, where civil war has raged since 2003 between local rebels and the pro-government Janjaweed militia. At least 200,000 people have died in Darfur from the combined effects of fighting, famine and disease, according to the United Nations.
More than 200,000 others have fled to refugee camps in Chad, where some have been attacked by the Sudanese military, the UN High Commissioner for Refugees said on Friday.

Copyright AFP (Agence France-Presse), 2006