South Sudan denied allegations it was arming rebels in two regions on its borders with Sudan.
Sudan reported South Sudan to the UN Security Council about violations, including the continued assistance to insurgents in the west and the south-east.
The Comprehensive Peace Agreement signed by both countries in 2005 stipulates that neither side should encourage rebellion against the other.
Sudan accused its neighbours of providing rebels with weapons and expertise in fighting the Sudanese army.
South Sudan however rejected the allegations, in turn accusing Khartoum of supporting rebels in the country.
"This accusation is false. (We) are not supplying anybody. The north are supporting rebels in the south and they want to cover it up," South Sudan's army spokesman Philip Aguer told Reuters by telephone.
"It should be the other way round. We should be complaining to the Security Council. We don't even have anti-aircraft missiles ourselves."
The regions concerned, Blue Nile and South Kordofan, used to be controlled by South Sudanese rebels during the civil war, but have been given to Sudan in the peace agreement.