Both sides have failed to establish the demilitarized zone despite agreeing to it in September 2012, the Sudan Tribune said.
Last Friday, Sudan and South Sudan reached an agreement on how to implement the zone, the Sudan Tribune said. Philip Aguer, the army's spokesman, announced the decision to withdraw the troops on Monday.
Aguer said troops are already moving away from the buffer zone so that they are six miles south of the border.
The withdrawal will be complete by April 5, the Tribune reported.