A UN security briefing obtained by Reuters on Wednesday morning reported about 20 deaths overnight.
Violence in the capital erupted on Monday when angry southerners took to the streets after the official announcement that former southern rebel leader and First Vice-President John Garang had died in a helicopter crash.
Police said on Tuesday that 46 people had been killed in the violence.
William Ezekiel, editor of the daily Khartoum Monitor with close ties to the southern community, said on Wednesday that
residents reported that 47 were killed overnight in the Khartoum suburb of Mamura, and 15 were killed in the district of Kalakla in the south of the city where violence had also been reported on Tuesday.
Those reports could not immediately be verified.
Ezekiel quoted residents as saying that gunshots and sirens could still be heard in some suburbs of Khartoum.
Aljazeera's correspondent in Khartoum, Al-Tahir al-Mardi, reports that police intensified their patrols of the town with armoured vehicles mounted with machine guns.
Many saw the police deployment as a too late move by the Sudanese authorities, adds al-Mardi.
The riots resulted in destruction of public and private property along with anger among the Sudanese people.
The riots caused extensive damage
to public and private property
"This is vengeance that has nothing to do with sadness, an aggression against an innocent citizen. I do have the right of citizenship in equal terms with those who had committed such acts," a Sudanese man whose home has been severely damaged told Aljazeera.
"Garang has died in South Sudan," another resident said. "We have lived here in peace. They broke into schools, terrified our children and even tore the clothes off from our little girls.".
The incidents have turned the country's mourning into a stand-off that some Sudanese fear will cause a rift between north and south Sudan, al-Mardi reported.
Call for calm
The new leader of southern Sudan met top US and South African envoys on Wednesday as part of diplomatic moves to maintain the country's fragile peace accord.
Salva Kiir, who took over the Sudan People's Liberation Movement (SPLM) after Garang's death, also pledged to fight for peace in the western region of Darfur.
Salva Kiir was appointed leader
of the SPLM
Assistant Secretary of State for African Affairs Connie Newman and the US special envoy to Sudan, Roger Winter, flew on Wednesday morning into New Site, a settlement in the south Sudanese bush where Garang's body is on view.
Washington has dispatched them to help efforts to maintain the January peace accord between the SPLM and Khartoum government in the north that ended 21 years of civil conflict.
"Enemies of peace may want to take opportunity of this situation so they don't allow the government and the SPLM to implement the peace agreement," Kiir said before going into a meeting with the US pair.
"So we are very much concerned about that and we would want to stop it and that is why we are appealing to all the Sudanese people to refrain from any hostility."
The US envoys were due to stay overnight in New Site before going onto Juba, also in southern Sudan. From there, they will go north to Khartoum to meet President Omar Hassan al-Bashir.