Phillip Aguer, a spokesman for South Sudan's Sudan People's Liberation Army, confirmed the meeting, the Sudan Tribune reported Sunday.
Aguer said the meeting would discuss "how to handle accusations and counter accusations" over which side was supporting rebels "fighting to destabilize or try to remove the other party in power."
"On our side, we have said time and again we do not provide any support to any armed groups, but the other side continues to make unfounded claims," he said.
A time and place for the meeting was not announced.
The SPLA's Maj. Gen. Mac Paul would co-chair the meeting, Aguer said, while Sudan's director of intelligence and security service could be the other co-chair.
Aguer said Juba had not received the names of the Sudanese delegation.
Controversy over the rebel groups last month caused Khartoum to announce it would close by Aug. 7 pipelines carrying crude oil from South Sudan.
Sudan agreed to extend the deadline by two weeks after prompting by the African Union and China.