Motupa, who spent last season on loan at Baroka, initially signed for Chippa United during the off-season as part of the deal that saw Linda Mntambo and Paseka Mako move to Pirates.
However, Motupa has since penned a three-year contract with the Students, according to a source close to the club.
"Motupa is a Wits player now. It's part of football business," says the informant.
"He signed a three-year contract and is due to start training with Wits today."
Motupa's manager Abbie Rasimphi confirmed Motupa has left Chippa and referred snl24.com/kickoff to the Clever Boys for further comment.
"I can't make an announcement on behalf of the team. I don't think that is good. Please speak to them," says Rasimphi of Liberate Resources Sports Management.