The APRM, part of the African Union (AU), is Africa's assessment for good governance.
Mbeki was one of the key speakers at the conference which was attended by ambassadors, diplomats, politicians, academics, NGOs and the media.
Mbeki, a powerful figure in African politics, headed the formation of the New Partnership for Africa's Development (NEPAD) and the transition to the AU. He has also played influential roles in brokering peace deals in Rwanda, Burundi, Ivory Coast, South Sudan and the Democratic Republic of Congo.
During question time, the subject of what practical steps the APRM was taking to help avoid future conflicts was put to the panel. The proverbial cat was thrown among the pigeons when a member of the audience questioned Mbeki as to what should have been done by the APRM ten years ago when xenophobia first raised its ugly head in South Africa .
The former president emphatically denied that South Africans were xenophobic. "There isn't a population of South Africans who attack other Africans simply because of their nationality," stated Mbeki to strong applause from some audience members.
To label these attacks as xenophobic is simplistic and fails to understand the underlying issues such as township thuggery, poverty, commercial competition, internal politics and foreign elements which are involved in crime, he said.
"South Africans have a long history of coexistence with other Africans. Mozambicans and Malawians have been coming to South Africa since the 19th century.
"In Alexandria Township there is a committee to protect foreigners. There is a population of 45 000 Ethiopians in Johannesburg that have never been attacked.
"Why are so many foreigners not attacked? Some foreign elements are involved in crime such as prostitution and drug dealing and when the police fail to take the necessary action, the community sometimes takes matters into their own hands," said Mbeki.
"There is also commercial competition. When the businesses of Somali store holders do better than their local competitors, sometimes the latter attack the Somalis and blame them for taking away their jobs."
He added that some of the violence in Pretoria was more about internal African National Congress politics than hatred of foreigners.
Mbeki also accused the media of mislabelling crime as xenophobia, pointing to an incident several years ago when a Mozambican was stabbed to death by three township thugs after they refused to pay for cigarettes they bought from his store and he physically challenged them.
"I doubt they even knew he was Mozambican."
But Emmanuel Mwamba, Zambia's High Commissioner to South Africa, responded angrily, accusing Mbeki of being in denial and making excuses for unacceptable behaviour and violence against foreigners – to loud applause from certain sections of the audience.
"It doesn't help labelling Nigerian drug dealers for example, as this builds prejudice against Nigerians instead of focusing on the fight against crime," Mwamba told the African News Agency (ANA) in an interview.
Following the verbal exchange, Mbeki offered to hold a meeting with African ambassadors to discuss the problem.
"I'm excited that the former president has agreed to hold the meeting and take up our concerns on this very serious issue. I'm also pleased that the minister of home affairs is getting involved," Mwamba told ANA.
"The structure and history of South Africa's economy demonstrates that poverty and inequality have to be resolved before blaming foreigners," he added.