Baxter has been linked with a move to PSL club Kaizer Chiefs and could be at the helm of Amakhosi by the time the season gets underway.
Bafana have 2019 Africa Cup of Nations qualifiers resuming in September and Baxter was using the recent COSAFA Cup in Polokwane to widen his pool of players for the upcoming qualifying campaign.
Bafana missed out on World Cup qualification with Baxter, who came in halfway through the campaign after Shakes Mashaba was shown the door by the South African Football Association.
“It obviously, especially from SAFA’s point of view, won't be ideal for the national team,” says Mokoena, who made over 100 appearances for the senior national team.
“If it is confirmed that he is leaving, it will not be good for South African football, especially the national team.”
Chiefs are expected to make an announcement of a new coach soon, having missed out on the likes of Patrice Carteron and Hossam El-Badry.