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As they moved to arrest Simon, he "collapsed". Paramedics were called to the scene and he was "declared deceased at the scene".
Speaking to the BBC on Monday, Nigeria's foreign ministry spokesperson Kimiebi Imomotimi Ebienfa described the incident as "a very unfortunate situation".
The Independent Police Investigative Directorate (Ipid) is now looking into what happened.
South Africa's Inter-Ministerial Committee on Migration, during its regular public update on the country's approach to migration management on Sunday, also confirmed that the matter was being investigated.
Justice Minister Mmamoloko Kubayi, who chairs the committee, said that during the police operation in Cape Town last Thursday "some foreign nationals... were resisting law enforcement operations".
In June, Nigeria's foreign ministry reported the death of Emeka Charles Iroegbu, also allegedly at the hands of South Africa's police. Ipid is also investigating that incident