The U.N. expressed its concern at the incident and condemned the forced relocation.
Abdul Haleem Mutaafi, governor of Khartoum state, on Wednesday said about 2,000 internally displaced people were scheduled to be relocated from Soba, a crowded area of the capital.
Mutaafi accused an opposition political party of inciting the citizens to anger by spreading rumors that even those with legal plots of land would be forced to move. He refused to name the party, saying all relevant information would be released after an investigation.
"There was a strong political mobilization and rumors that all persons in the areas would be relocated and moved out of the areas," Mutaafi said.
He said police who had gone to the area to implement the relocation were met by a huge crowd and ordered to return to the station.
The mob, he said, attacked a passing police van transporting inmates, killing one court policeman and snatching two rifles.
The crowd then moved to Azzahari Quarter police station, about a kilometer away, where they besieged and burned down the whole building, killing 13 policemen. He said 13 others were hospitalized.
The United Nations expressed "deep concern" about the incident. Radhia Achouri, U.N. spokesperson, said they had received reports that security forces opened fire on the crowd who had gathered at a bus station. She told a weekly press briefing that the number of casualties was unknown.
Police denied using their weapons, saying the three civilians died in the crush when police tried to push the crowd away from the station.
"None of those citizens was killed by a firearm," Maj. Gen. Tarek Mahjoub, director of the Khartoum State Police Force, told reporters.
The governor said reorganization of the capital would continue and there were other plans to move displaced people to camps outside the city.
Achouri condemned the forced relocation of the displaced people.
"Every attempt must be made at this time to stop demolitions and relocations, until suitable alternative arrangements (acceptable to the affected IDPs) are made. In all instances, forced relocation must end in the interests of protecting rights and livelihoods and preventing loss of life." she said.