Thursday's withdrawal would ease tensions in the area bordering Eritrea.
Ali el-Safi, the Eastern Front spokesman, said: "They are seeing the government forces withdrawing to the northern part of the area from where they came.
"They have left the town but we are not sure if they are regrouping to attack again or fully withdrawing."
The 3000 soldiers and four tanks rolled into Hamesh Koreb on Wednesday and took up positions 200 metres from the former southern rebel Sudan People's Liberation Movement (SPLM) who also have troops there.
The incident caused a stand-off which may jeopardise a north-south peace deal signed between the two sides last year.
The SPLM could not immediately confirm the withdrawal of government troops from the town.