Bafana are set to depart for Ndola, Zambia on Tuesday morning to take part in a four-nations tournament, which includes the host nation along with Zimbabwe and Angola, in the coming days.
Baxter last week revealed that Mokwena had been invited to partake in the national team camp as part of a program that will empower up and coming South African coaches.
However, the Buccaneers have since turned down the request to release their sought-after tactician during this international break.
“Rhulani is not going to be taking part in our camp. We understand the situation that Pirates are in [in the Absa Premiership title race],” Baxter told the media on Monday afternoon.
“As everyone knows, this camp has been really compromised in terms of time for preparation. The warning times for us to know we were taking part and leaving was very, very short.
“What that has done is that it’s also made the lines of communication a little bit shorter, and it’s possible that protocol wasn’t followed 100 percent.”
In providing more clarity, Baxter explained that Pirates are indeed open to lending Mokwena’s services to the national team, but the notice period and timing of the call is what prompted their refusal.
“You know, I got confirmation of the camp 10 days before we were due to leave, so the actual ‘negotiations’ – if you want to call it that – for the camp were protracted. Therefore everything had to go very quickly,” he stated.
“Possibly, in a normal world, we would have given Pirates greater notice, and they felt a little bit that it was sprung on them. That’s understandable because they’re in a pressure situation at the moment.
“But, we’re all agreed on that the concept is a good one and we want to do it, and Rhulani is a good candidate. So, no one’s arguing, it’s just a question of making sure we do it at the right tempo that suits everybody.”
South Africa under-20 coach Thabo Senong has since been recalled to assist the senior team, having to withdraw midway through a SAFA coaching instructor's course he had been attending since last week.