Mbalula said in his department's budget vote speech in Parliament he was aware the SA Rugby Union (SARU) was involved in "complex" negotiations around the issue.
"We are aware that SARU is involved in complex negotiations that embody a number of fundamental dilemmas concerning the promotion of the Kings to Super Rugby," Mbalula said.
"It is important that SA Rugby urgently finds an amicable solution as the cloud of uncertainty and anxiety is weighing very heavily on the players and franchises which will be affected and impacted upon by their decision." SARU has promised the government that it would field a sixth team - the Southern Kings - in next season's Super Rugby tournament.
The Southern Kings have been mooted as a "black" Super Rugby team aimed at developing rugby in the Eastern Cape. They however recently appointed two New Zealand coaches and named Luke Watson, a white player, as captain.
SARU promised the Southern Kings they would be included in Super Rugby from next season, but this meant one of the existing South African teams would have to drop out of the current tournament to make space for them.
South Africa, New Zealand and Australia Rugby (SANZAR) chief executive Greg Peters has ruled out South Africa's wish to have six teams in the tournament.