Mapisa-Nqakula was answering questions in the National Council of Provinces on Tuesday where she said there were other investigations into the assault of members of the public by the army in different parts of the country.
The army was accused of killing Khosa during the start of the lockdown in March.
However, Mapisa-Nqakula said while the other cases were referred to the police because they were assault charges, the Khosa case is handled by three different bodies.
She said the Khosa matter was probed by the Military Ombud, the Board of Inquiry and the police and military police.
She said she hoped a report will be ready in the next few weeks.
She said she was still ashamed by incidents of the brutality of the army against civilians.
“Anything that happened to members of society, if there is any wrongdoing, if anything associated with that structure you get ashamed, you get embarrassed. Even in the matter of the Khosa I am record saying as the South African government we hang our heads in shame for the loss of life. I am single out this case in particular because it is a matter of interest in South Africa,” said Mapisa-Nqakula.