Sudan's military accused Juba of supporting rebels from Darfur after Khartoum's troops clashed with the insurgents in part of the war-torn region near the border between the two countries Sunday.
The army said the Justice and Equality Movement -- one of several groups battling Sudanese forces in Darfur since 2003 -- used South Sudan's Bahr al-Ghazal region as a base to enter neighboring Darfur on Sunday, where the two sides clashed.
"The government of South Sudan has continued harboring and supporting the terrorists," military spokesman Colonel Al-Sawarmy Khaled Saad said in a statement.
"We have raised the matter with the government of South Sudan, warning of the seriousness of these violations," Saad added.
The military and JEM gave conflicting accounts of the clashes, with both claiming to have inflicted heavy losses on the other side in the fighting in the Tullus area, southwest of South Darfur state capital Nyala.
Saad said the army, along with the controversial counter-insurgency Rapid Support Forces, laid ambushes along the roads used to enter South Darfur state, capturing 100 JEM vehicles and killing many fighters.
JEM spokesman Jibril Bilal said there had been "a decisive battle with government forces" but that the military's account was "completely false."
He told AFP by phone that rebels had captured a government military camp and "hundreds" of their troops.
Darfur erupted into conflict 12 years ago when ethnic insurgents rose up against President Omar al-Bashir's Arab-dominated government, complaining that they were being economically and politically marginalized.
Khartoum has already accused South Sudan of supporting rebels in the South Kordofan and Blue Nile areas.
The south seceded in 2011 under a peace deal that ended 22 years of bloody civil war, and around the same time the Sudan People's Liberation Army-North launched its campaign against Khartoum in South Kordofan and Blue Nile.
South Sudan has also faced its own civil war since 2013, and accused Khartoum of giving support to rebels.
Khartoum and Juba deny each other's allegations.
The United Nations says that since the conflict in Darfur started, more than 300,000 people have been killed and another 2.5 million forced from their homes by the unrest.
The International Criminal Court has indicted Bashir for alleged war crimes, crimes against humanity and genocide in the western region.
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