The clashes occurred between troops loyal to former Sudan People's Liberation Army Lt. Gen. George Athor and Southern Sudan's army as the region prepares for independence after voting to secede from the north, the BBC reported Friday.
Athor has been leading a rebellion against the SPLA from his base in Jonglei state, where many of the fatalities occurred.
Southern army spokesman Philip Aguer said Athor's troops attacked SPLA soldiers Wednesday and Thursday, killing 20 members of the security forces. He said about 30 of Athor's troops also died. One unconfirmed report said at least 39 civilians were killed.
Athor took up arms last year after alleging fraud in state elections, but agreed to a cease fire just before a referendum in which 99 percent of the voters said they wanted to secede from the north.
On Wednesday, Sudan's U.N. ambassador suggested an arrest warrant by the International Criminal Court for Sudan President Omar al-Bashir for alleged war crimes be dropped as a "reward" because he agreed to accept the outcome of the vote to secede.
The charges against Bashir are related to a separate conflict in the western region of Darfur.
Southern Sudan will become the world's newest independent state on July 9.