South Sudanese President Salva Kiir ordered military forces from the border to prepare for the establishment of a demilitarized zone.
Philip Aguer, a spokesman for the South Sudanese military, said the president's orders will be completed by April 5.
"Troops have started moving to the designated areas away from the buffer zone," he was quoted by the independent Sudan Tribune as saying.
South Sudan gained independence in 2011 under the terms of a 2005 agreement that ended the Sudanese civil war. A year later, both sides nearly went to war because of disputes over border territories.
Sudan and South Sudan last week agreed to the demilitarized zone. South Sudanese military officials called on their Sudanese counterparts to hold up their end of the bargain.