"The attackers totally burnt down these places and killed several of the civilian population. Between 6,000 and 8,000 people are out in the open, without shelter and deprived of everything," said the statement, signed by Hourmadji Moussa Doumgor, Chad's communication minister.
The raids appeared to be the latest spillover of violence from Sudan's Darfur region, where more than 200,000 people have been killed since 2003 in a war between rebels and Sudanese government forces and their allied fighters.
But the Sudanese government denied any responsibility for the raid.
"I have not heard anything about this incident. The Sudanese government played no role in this whatsoever," Ali al-Sadig, a Sudanese foreign ministry spokesman, told reporters in Khartoum.
Idriss Deby, Chad's president, who also faces internal fighting in the east, frequently accuses Sudan of sending the Janjawid - mounted raiders whose name in Arabic means "devils on horseback" - across the border on raids.
Sudan's government routinely denies this but has refused to allow the deployment of a strong United Nations force in Darfur to bolster an over-stretched African Union peacekeeping contingent on the ground there.
The Chadian government said: "Chad wants peace on its borders but will assume its duty to protect its citizens by every appropriate means if Sudan does not do its part to end these armed militia attacks against the Chadian population of the border region."
Ban Ki-moon, the UN secretary-general, recommended in January sending up to 11,000 peacekeeping soldiers and police to Chad and the Central African Republic to secure their borders with Darfur and protect civilians and refugees.
But Chad has said it wants only a civil protection police force in the east, where hundreds of civilians have been killed since last year in cross-border raids from Sudan and ethnic fighting between Arabs and non-Arabs.