His actions were condemned by the majority of the South African soccer community, but Motaung believes the gloveman had legitimate back pain on Sunday and has confirmed he was in hospital until Wednesday.
Motaung added that Khune may not be fit in time for Sunday's PSL clash with Black Leopards.
He told the Sowetan: "Khune complained about back pains on Sunday and had to be admitted to hospital. He was only released on Wednesday.
"I have my doubts if he will play this weekend because he missed training this week. I am aware that he appeared to have been faking injuries.
"But I cannot go into those details because I am not a referee. But he was indeed in pains when I saw him on Sunday."