The Justice and Equality Movement (JEM), a Darfur-based group which is part of a wider rebel alliance seeking to topple the government, said it ambushed a convoy north of Dilling town.
The army spokesman could not be reached for comment.
There has been an upsurge of rebel activity since April in the South-North Kordofan boundary region, through which passes the main road link to the national capital Khartoum.
Dilling is on the route linking the South Kordofan state capital Kadugli with El Obeid, North Kordofan's capital which is home to an air force base and an oil refinery.
"Authorities ordered buses travelling to El Obeid to cancel their trips," one resident said, asking for anonymity because of the situation.
On Wednesday, both the JEM and the army said they had fought at Sidrah, about 130 kilometres northeast of Dilling in North Kordofan.
That attack ended weeks of relative calm in the area.
It came as the African Union and East Africa's regional bloc, the Inter-Governmental Authority on Development (IGAD), launched a panel to probe allegations by Sudan and South Sudan that each is supporting rebels operating on the other's territory.
JEM spokesman Gibril Adam Bilal said that after the ambush, surviving government troops fled towards Dilling where fighting continued on the town's outskirts.
He said six government troops were killed, but analysts say casualty figures from either side in the war should be treated with caution.
The rebels also took some prisoners, Bilal said.
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