"A (northern) Sudanese Armed Forces Antonov aeroplane bombed two areas in the west of Raja county in Western Bahr al-Ghazal state on Monday morning," said Philip Aguer, spokesman for the Sudan People's Liberation Army (SPLA).
"People were very surprised, because there was no warning, but very fortunately there were no casualties."
The northern army was not immediately available to respond to the charges.
The former civil war enemies in north and south Sudan have traded bitter accusations since a January referendum on independence for the south, where the population voted almost unanimously to break away and form their own nation.
The area where the alleged bombing occurred borders the north’s war-torn Darfur region, where fighting continues between rebels and Khartoum.
The northern army has accused the south of aiding Darfuri rebels, claims rejected by the south.
"There are no rebels there and you will have to ask them (the north) why they are carrying out these attacks," said Aguer.
"Darfur borders the state, but the border is a long way away."
However, he said the southern army would not take any retaliatory action.
"We are only protesting at these attacks, and asking them never to happen again," Aguer said.
The north was accused of launching similar bombing raids in November and December last year.
It also rejected those accusations, but did admit one "accidental" bombing raid on southern territory that it claimed was in pursuit of Darfuri rebels.
Earlier this month, southern officials revealed documents they said detailed northern arms shipments to southern militias, after a wave of deadly clashes in the south.
Khartoum has repeatedly rejected all such accusations, and claimed the documents were fabricated.
Several hundred people, many of them civilians, have been killed since January's referendum, in fighting between the SPLA and rebel militias in Jonglei state and the oil-rich Upper Nile and Unity states that both border the north.