Nyathi was set on fire by an angry mob looking for illegal aliens in the community on Wednesday night.
He visited the area again on Thursday in a bid to ease tensions between community members and foreign nationals.
The community has accused undocumented foreign nationals of being behind a string of violent crimes, including rape and murder.
At least four South Africans were killed in the community over the weekend.
Speaking to the media on Thursday, Cele said tackling crime in the area was made more difficult due to the narrow streets and dense population.
“The flaws in this area are the life of this area itself. As police we have always raised the issues we suffer from environmental design, this is an area for police that takes some time to respond.
“We raised the matter with Prime Minister David Makhura yesterday and was told that not all the lights were working either, but we want to believe that despite what has happened here the situation will improve.”
National Commissioner Fannie Masemola has denied claims that the situation is out of control.
“We have delivered around 16 vehicles to the area and there are around 120 police officers deployed in the area. All the commitments we made yesterday have been kept. There are police in the area and we have delivered these vehicles.
“There is no situation out of control. The fact that there is someone who died does not mean that the situation is out of control, we are still managing the situation, it is a manageable situation” , did he declare.
Police arrested 24 people overnight, although no one is in custody for Nyathi’s murder.