Amajita last night arrived in South Korea 10 days before the FIFA tournament starts to acclimatise to conditions in Suwon.
However, the Thabo Senong-led side are without Mokoena and Bidvest Wits striker Phakamani Mahlambi and defender Reeve Frosler - prompting Sports Minister Thulas Nxesi to intervene at SAFA's request.
Wits are reluctant to release Mahlambi and Frosler before their final league game against Chiefs on May 27 given that they are two points clear of champions Mamelodi Sundowns at the summit with two matches left.
Meanwhile, SuperSport still want Mokoena to help them push for a top-three finish in the league and compete for honours in the Nedbank Cup and CAF Confederation Cup.
"You are asking a politically loaded question because that goes to the issue of club versus country and the rules of FIFA in terms of is it an automatic release," said Baxter, whose side open their Confed Cup Group D campaign against Horoya AC at Lucas Moripe Stadium tonight (19h00).
"These are legal things I think discussed above my head at this moment. All I can say in principle, the ambition of SuperSport is to support national teams, be it the Under-20s, U-21s, Olympics team and senior team, and that's our ambition. At this moment we have released lot of players to the U-20s.
"Tebogo is a different case because he is a senior player. He is a senior player playing regularly, same as the Wits players. The question being asked: must we release him or can we discuss when can we release, because we have a few players and a lot of commitments."
Baxter, who will take charge of Bafana Bafana for the second time at the end of the season, has indicated he will touch on the club versus country issue when he shares his vision for the national team at a press conference on Monday afternoon.