The Ministry of Foreign Affairs will discuss border issues with Sudan under a forum established under the 2012 Cooperation Agreement, an official has said.
Sudanese authorities officially closed the border earlier this week and prevented all South Sudanese from crossing.
The closure followed a threat to do so over alleged support of the South Sudanese government to the Sudanese rebels.
However, the government in Juba has been denying the claim.
Foreign Ministry spokesperson Amb Mawien Makol says the two sides will discuss the matter under the Joint Political Security Mechanism.
“The time is now to sit again and discuss the issues of dispute, those accusations,” Amb Makol told Eye Radio.
Before the closure, UN agencies said South Sudanese were crossing to Sudan due to hunger and insecurity.