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 KickOff.com 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.
Meanwhile, Wits have handed a trial to Zambia international Moses Phiri, while veteran attacker Daine Klate will likely play his football elsewhere this coming season.
The Telkom Knockout champions have also added Deon Hotto, Bantu Mzwakali, Mxolisi Macuphu and Brighton Mhlongo to their roster ahead of 2018/19.