In a statement, the National Intelligence and Security Service (NISS) said South Sudanese President Salwa Kiir, his deputy Taban Deng and top army commanders held meetings last week with the SPLM-N rebel group.
The group -- the Sudan People's Liberation Movement-North (SPLM-N) -- is fighting Khartoum's forces in Blue Nile and South Kordofan states.
"These meetings were aimed at extending the war in Sudan," NISS said.
"South Sudan continues to host Sudanese rebels."
As part of this policy, Kiir and Deng held "intensive" meetings with SPLM-N in Juba between Wednesday and Saturday, NISS said.
"We are warning the South Sudanese government to stop intervening in Sudanese affairs," NISS said.
It bitterly contrasted South Sudan's policy with Khartoum's humanitarian aid to hundreds of thousands of South Sudanese refugees who have arrived fleeing war and famine in their own country.
"While Sudan has opened its borders to South Sudanese citizens, the government of South Sudan is responding by hosting Sudanese rebels," NISS said.
Officials say that during his visit to Khartoum in September, Deng had given assurances that Juba would expel rebels fighting Sudanese forces.
Armed revolts on both sides of the border have soured relations between Khartoum and Juba.
South Sudan split from Sudan in 2011 under a peace deal that ended a 22-year civil war.
But Juba and Khartoum have traded allegations of supporting each other's rebels on their territory, charges which both countries deny.
South Sudan, the world's youngest nation, fell into a brutal civil war in December 2013.
Tens of thousands of people have been killed in the country since then and more than two and a half million people driven from their homes.
Sudan is hosting about 380,000 South Sudanese refugees who have arrived since the war erupted, the UN's refugee agency says.
The influx has swelled in recent months after South Sudan declared a famine in parts of the country.
In late March, Sudan opened a "humanitarian corridor" for delivering food aid to thousands of South Sudanese suffering from famine in Unity State and Bahr El Ghazal.
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