The 12 men belonged to the South Sudan Defence Forces (SSDF), the southern militia led by General Paulino Matip, a regional commander who changed allegiances several times in the course of the 21-year north-south civil war, Al-Sudani newspaper said on Thursday.
In January, Matip announced that the militia had disbanded and joined the ranks of the Sudan People's Liberation Army (SPLA), formerly the main separatist group and now a partner in the country's national unity government.
Major-General Elias Weah of the SPLA was quoted by the newspaper as saying: "Twelve persons were found dead and 26 others seriously wounded near the town of Abyei in an ambush set up for about 500 people belonging to General Paulino Matep who were travelling from Khartoum to join the SPLA in the south."
He accused armed men from a faction of the SSDF of carrying out the ambush on unarmed elements of Matip's group, who were driving on six vehicles which were "completely" destroyed in the ambush.
"Moreover, a large number of the attacked militias were missing," Weah said.
No official source was available to confirm the incident.
A peace agreement was reached a year ago between the Islamist government of Omar al-Bashir, the president, and the southern rebels, ending Africa's longest-running civil war, which killed 1.5 million people and displaced four million.
The agreement demanded that the various militia groups in the south disband or join either the Sudanese national army or another armed wing.
Former militia leaders are now
partners in Sudan government
The fate of the Abyei region, an oil-rich territory that is the site of a dispute between two tribes, was one of the main stumbling blocks in the north-south peace deal and special provisions now apply to the area.
The UN is currently deploying about 10,000 troops to Sudan's south to monitor the implementation of the peace deal.
In other news, on Wednesday thousands of Sudanese paralysed the streets of Khartoum protesting against any deployment of UN troops to the violent western Darfur region.
The government and opposition parties have all said they do not want that UN force to extend to Darfur as well.
UN sources say any UN force in Sudan's west is likely to keep the same AU forces on the ground, but change the command over to a UN peacekeeping mission.