Mokwena’s side suffered a 2-0 defeat to Mamelodi Sundowns, a result that eliminated them despite only needing a draw to secure a place in the quarterfinals.
The former Sundowns mentor believes the setback reflects deeper structural issues within Algerian football, warning that local clubs will continue to lag behind their continental rivals unless fundamental changes are made.
"I hope the Algerian football officials allow us to come in for a debrief at the end of the season as technical people involved in the game because the results continentally should be a little bit of a worry not just this season but overall for the last couple of years,” Mokwena said.
“When I talk, not only at club level but also at international level, AFCON and the likes and generally the teams that do well on the continent, generally have a very, very strong league.
“The Algerian league is quite strong, to go to El Bayadh is very, very complicated, there's a lot of physicality, there's some very good players with very good backgrounds. There's some players at MC Oran, you see the level of some of those players is incredible."
Mokwena made attempts to sign at least five players during the recent January transfer window, but the rules in Algeria were a stumbling block.
"There are a lot of cohibiting and challenging factors that allow the league to be stronger so that the teams are stronger and the teams that are stronger then are able to produce players for the national team and that makes the teams a little bit stronger,” the coach added.
“If you look at most of the players except for one or two in the AFCON are always overseas based players and that doesn't always mean you have the strongest team. If you check even the Morocco team and the team, apart from Egypt who have a few local based players but where the challenges come, for me, number one is the size of the squad.
“It's impossible to have a 22-man squad with a number of games and the amount of travelling. To be limited only to 22 players plus five younger players and you see I don't play the younger players because of injuries or because of anything like that, I play the kids.
“We've played more of the U23 players more than any other team but we play the kids because also we are limited with options in relation to the squad size so when injuries happen and fatigue and the accumulation of games comes into play, you have a few challenges."