Luka Biong Deng, a minister of cabinet affairs, resigned after Khartoum declared Abyei a "northern town" and dismissed international calls to pull its troops out of the district also claimed by the soon-to-be independent south.
"We had hoped that we could form two viable states in good relationship with each other, but those in Khartoum do not seem interested in peace," said Biong Deng, who hails from the Abyei area and is a senior leader in the south’s ruling party.
"But with war crimes being committed in Abyei at the hands of the (Khartoum’s ruling) National Congress Party, I could not in good faith continue to take part in such a government," he said.
The United Nations meanwhile condemned attacks on the flashpoint district, and urged both Khartoum and the southern Sudan People's Liberation Army to negotiate an end to the crisis.
The UN human rights chief Navi Pillay said: "This is certainly no way to advance the peaceful coexistence of north and south Sudan.
"I am particularly alarmed by the shelling of civilian areas in Abyei by the Sudan Armed Forces, as well as reports of aerial bombardment in other locations such as Todacch, Tajalei and in the vicinity of the River Kiir (Bahr al-Arab) bridge.
"I urge all parties to explore a negotiated solution to the Abyei crisis and to avoid a descent into further conflict and chaos," she said, adding that all rights violations must be investigated and perpetrators brought to justice.
Khartoum's defence minister, Abdulrahim Mohammed Hussein, said however that "Abyei will remain a northern town until the population decides on their situation by themselves," the official SUNA news agency reported.
Abyei, a fertile border district claimed by both north and south Sudan, was due to vote on its future in January alongside a referendum on independence for the south, which delivered a landslide for secession.
But Abyei's plebiscite did not happen amid arguments as to who was eligible to vote, and northern troops and tanks overran the contested area on Saturday.
"The (northern) army will stay in Abyei in order to maintain security and stability until a political decision is taken," Hussein added.
A UN Security Council delegation was due to hold talks on Tuesday with southern president Salva Kiir in the regional capital Juba.
The southern government has demanded that the north's Sudan Armed Forces (SAF) withdraw immediately.
"The SAF must end their illegal occupation and leave Abyei," the south’s information minister Barnaba Marial Benjamin said.
In Geneva, the UN Office for the Coordination of Humanitarian Affairs said there were roughly "15,000 people displaced in and around Agok town," about 40 kilometres (25 miles) south of Abyei.
The United Nations said the refugees, mainly southern-supporting Dinka Ngok people, fled across the border as armed looters set fire to houses in northern-controlled areas.
Heading in the opposite direction -- and in large numbers -- southern officials say, are pro-northern Misseriya, a cattle-herding people who traditionally move through Abyei each year with their animals seeking pasture and water for their herds.
"Misseriya tribes are being brought into Abyei with the support of the Sudanese government, with the intention of occupying the Dinka Ngok territory to justify their participation in the referendum," Benjamin charged.
"Nobody can entertain the idea of a Kashmir or a Western Sahara scenario in Abyei," Benjamin added.
However, senior Misseriya leader and politician Sadiq Babo Nimir dismissed reports his people were moving into Abyei.
"It is nonsense, because this is the time of year the Misseriya move north, to follow the grazing there," he said.
"This is a clash between two armies, and the Misseriya are not involved," Nimir added.
The north's seizure of Abyei, in the run-up to international recognition of southern independence in July, has been condemned by the world powers as a threat to peace between north and south Sudan.
The United States urged Sudan to withdraw its forces from the district and warned their presence would jeopardise lucrative US efforts to normalise ties with Khartoum.
"We think those (northern) forces should be withdrawn," the US envoy for Sudan, Princeton Lyman said on Monday.
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