Auger said 65 rebels were killed in Sunday’s clashes between the Southern People’s Liberation Army (SPLA) and members of a militia group lead by Ulony, which he accused of being in the service of the Sudanese government.
He said the army had recovered assault rifles that he said had been "definitely" been supplied by the north.
Aguer said that members of another militia, this one loyal to the renegade general George Athor, attacked the SPLA in Jonglei state on Monday, and the army responded by attacking two of their camps.
Athor confirmed that there had been heavy fighting at two of his camps in northern Jonglei, and said 172 southern soldiers had been killed.
Aguer said only seven soldiers had died.
South Sudan, which is due to become an independent country in July, is facing the possibility that Ulony and Athor are joining forces in a coordinated rebellion in the region.