South Sudan's ruling party said on Friday it would not recognise an election in the north's main oil state and would not serve in its parliament or government because it said Khartoum rigged the vote.
The state of Southern Kordofan will stay with the north but analysts say any talk of fraud could spark violence between supporters of the southern Sudan People's Liberation Movement (SPLM) and the northern ruling National Congress Party (NCP).
South Sudan voted to declare independence from Khartoum in a January referendum promised in a 2005 peace deal that ended decades of civil war with the north. The split is due in July.
Southern Kordofan held the governorship vote more than a week ago but no results have been announced.
Many of the state's population fought alongside southern rebels during the civil war and fear they will be targeted in the new, separate north Sudan. The vote was delayed from April last year after the SPLM accused Khartoum of rigging a census.
"We will not recognise the election in South Kordofan because the National Election Commission (NEC) is a tool of the NCP and trying to rig the vote," said Yasir Arman, head of the northern section of the SPLM.
"We will not participate in the parliament or (future) government in South Kordofan because we have proof the vote was rigged," he told Reuters.
The NEC rejected the accusations and said counting would continue without the SPLM, with initial results expected on Saturday afternoon.
"If any parties have any objections or see violations they should go to the courts and not make press statements ahead of the results," said NEC spokesman Abu Bakr Waziri.
There was no immediate reaction from the NCP which has fielded as governor candidate Ahmed Haroun, a man wanted by the International Criminal Court over charges of war crimes in Darfur.
Khartoum is due to lose control of up to 75 percent of the country's 500,000 barrels per day oil production when the south leaves.
Southern Kordofan holds the most productive fields left in north. It is also key to Khartoum because it neighbours Darfur and the disputed, oil-producing Abyei border region, another possible north-south flashpoint in the build-up to secession.
Sudan's President Omar Hassan al-Bashir held onto power in last year's election and his NCP won an overwhelming victory in the north. The SPLM dominated the south.