A rebel army official said about 3000 army soldiers and four tanks entered the eastern town of Hamesh Koreb on Wednesday morning and took up a position 200 metres from the former southern rebel Sudan People's Liberation Movement (SPLM) position.
"This is a violation," SPLM acting military spokesman Elias Waya Nyipuocs told Reuters. "But we have instructed our soldiers not to open fire."
Earlier, eastern rebels said they had been attacked in the rebel-held Hamesh Koreb area by Sudanese armed forces. Nyipuocs could not immediately confirm that.
Despite the year-old peace deal between Khartoum and the SPLM that ended two decades of civil war in Sudan's south, conflict simmers in the east and in the western region of Darfur.
Under the peace accord signed in January last year, a coalition government was formed with two separate armies for the north and south. Joint army units are also being deployed in most major towns and the capital Khartoum.
SPLM troops were supposed to have left Hamesh Koreb town by 9 January this year, but Nyipuocs said they had already informed the United Nations and the Sudanese army that they faced logistical problems and would not meet the deadline.
He said the SPLM had issued an ultimatum to the Sudanese armed forces to pull back their forces from Hamesh Koreb by the end of the day or they would withdraw all SPLM forces from the joint units and order them to return to their bases.
"It is tense ... the Sudanese armed forces may provoke our forces ... but we have strictly ordered them not to open fire," he added.
Sudanese army officials were not immediately available to comment on the stand off.