Pareq Osman al Tahir, director of police in Khartoum, told reporters on Wednesday, that 14 police officers had been killed and 13 injured, while three civilians were killed and 11 injured.
Other sources on Thursday disputed the number of the dead.
"The fighting between the police and the community has been going on until this morning, and I can see the police office and the office of the Public Committee [the office responsible for the organisation and registration of IDPs] burning," Karak Mayik Nyok, executive director of the local women’s organisation, Diar for Rehabilitation and Development Association, told IRIN on Thursday.
"Twenty IDPs were killed and many, many were wounded. Most people are fleeing to Mayo Mandela camp [about 15 km away]," Nyok, who said she was talking to IRIN while standing outside the camp, said. "The fighting [however] has stopped."
The governor of Khartoum State, Abdel-Haleem Al Mutafi, had on Wednesday told a news conference that the police did not shoot at the IDPs.
"The police station was surrounded by a massive amount of people with weapons, simple traditional weapons like knives and axes," he said. "The people wounded were not shot. The police did not fire."
Sources said the unrest began when trucks loaded with armed men rolled into Soba Eradi, an IDP camp housing 26,000 people, at 5 a.m. (0200 GMT) on Wednesday morning.
Kirsten Zaat, UN advocacy officer in Khartoum, told IRIN the aim of the operation was to move the IDPs to Jebel Alial and El Amal town, about 50 km south of Khartoum.
Other sources said the IDPs did not want to be relocated. They gathered at a local bus station to protest, but at about 9:40 a.m. (0640 GMT) the police officers opened fire on them, the sources told IRIN.
The situation escalated as IDPs confiscated weapons from security forces, the sources added. Hundreds of IDPs fled the area, and unknown assailants set fire to the local police station and IDP shelters.
Many IDP women left the camp early on Wednesday morning to clean houses in Khartoum and could not return to their homes when they came back to Soba Eradi, Nyok told IRIN.
"The police [are] letting women in, every now and then, to look for their children," she added. "I’m waiting for permission to go in and look for the seven children of my uncle and take them to Mayo Mandela."
The majority of the IDPs in Soba Eradi were Dinka from Bahr al Ghazal and Equatoria in southern Sudan. There were also Shilluk and Nuer from Upper Nile and some IDPs from Darfur.
"Security forces already demolished their houses in August 2004, during the rainy season, and they have lived in shelters ever since. They have no houses," Nyok said.
Radhia Achouri, spokeswoman for the UN Mission in Sudan, told reporters on Wednesday that the UN did not seek to dispute facts on the ground as represented by the various parties.
"The UN supports the government's intention to replan identified current locations of displacement," she said. "However, the process by which demolitions, relocations and plot allocations are being undertaken constitute human rights violations, including forced return."
She added: "Every attempt must be made at this time to stop the demolitions and relocating until suitable arrangements acceptable to affected IDPs are made. Forced relocation must end in the interest of protecting rights and livelihood and preventing loss of life."
She reminded the government of Sudan of its international legal obligations to guarantee the security and safety of all Sudanese civilians.
The UN Office for the Coordination of Humanitarian Affairs in Khartoum, in statistics compiled on 11 March 2005, put the total number of IDPs in official camps and squatter areas in Khartoum at 2,072,320.