But he defended the decision of his organisation's Appeal Board to award the Africa Cup of Nations title to Morocco after upholding their protest over the outcome of the January 18 final.
Senegal, who won the match in Rabat 1-0, had walked off for 14 minutes at the end of the regulation time in protest of hosts Morocco being awarded a penalty but returned to win in extra time.
While Morocco's initial protest had been rejected by CAF's Disciplinary Board, the same governing body's Appeal Board found Senegal had transgressed tournament regulations by staging a walkoff and handed Morocco the title.
"I previously expressed my extreme disappointment with the incidents that took place at the final," Motsepe said in a video statement released on Wednesday.
"It undermines the good work that CAF has done over many, many years to ensure that there's integrity, there's respect, there's ethics, there's governance, as well as the credibility of the results of our football matches.
"We are still dealing with suspicion and mistrust. It's a legacy issue. When I became president, one of the major concerns was the impartiality, independence and the respect of referees and match commissioners, and a lot of good work has been done," he insisted.
Motsepe highlighted that both of CAF's disciplinary and appeal boards were independent entities made up of legal practitioners chosen with the help of member associations.
"It is important that the decisions of our Disciplinary Board and Appeals Board are viewed with respect and integrity," he said.
"If you look at the composition of those bodies, they reflect some of the most respected lawyers and judges on the continent.
"But we will still have to deal with this perception and concerns about the integrity. It's an ongoing issue."
Motsepe said CAF was committed to fair play and denied there was any preferential treatment amid perceptions that Morocco have too much sway over the African game.
"I'm told that Senegal is going to appeal, which is very important. Every one of the 54 nations in Africa have a right to pursue appeals and we will adhere and respect the decision that's taken at the highest level.
"A critical factor is that not a single country in Africa will be treated in a manner that is more preferential, or more advantageous, or more favourable than any other country on the African continent," the South African billionaire mining magnate added.
