"The government is committed to protecting property and lives of citizens in the event that rebels threaten security and stability," Information Minister Abdul Basit Sebdarat told the official SUNA news agency.
He added that the government "did not use aircrafts, it did not carry out any aerial bombings in any region in eastern Sudan, saying the rebel claims were "not correct."
Two rebel groups in the region had said that the government has launched an intensive aerial bombing campaign on civilian targets in eastern Red Sea and accused it of pursuing a policy similar to that used in the troubled western Darfur region.
The groups, which attacked government positions south of Port Sudan Sunday and claim to have made significant advances since, said the bombing began in the Barka Valley on Thursday.
They added that it resulted in a large but unknown number of civilian casualties who filled hospitals in Port Sudan and the town of Tokar, 120 kilometers (75 miles) south.
A Sudanese military spokesman acknowledged that troops were active in the area, but insisted that the operation was aimed at combing the region and "pursuing remnants of rebel forces that had attacked Doleib Yai in Tokar."
The Eastern Front was created only in February by eastern Sudan's two main dissident factions, the Beja Congress and Free Lions. It launched its first major military operation against the government on Sunday near Tokar.
Both the eastern and western groups claim their regions are being marginalized by the Arab-dominated government in Khartoum. The government accuses Asmara of providing military support to the rebels, charges Eritrea denies.
The new fighting has sparked fears that a second Darfur-type conflict will open up in Sudan even as peace talks between the western rebels and Khartoum are underway in Nigeria.