The Miss Universe Organisation on Tuesday put out a statement to rebuff Mr Harfouch's claims, saying that "no external group has been authorised to evaluate delegates or select finalists".
It suggested that Mr Harfouch may have been referring to the Beyond the Crown programme: a "social impact initiative" that operates independently from the Miss Universe competition, and has a separate selection committee.
The Miss Universe Organisation announced the Beyond the Crown selection committee on Monday. In its statement on Tuesday, the organisation said that Mr Harfouch's allegations had "mischaracterised" the programme.
Mr Makélélé, who also announced his resignation via Instagram, described it as a "difficult decision".
"I hold Miss Universe in the highest regard. The platform represents empowerment, diversity, and excellence - values I have always championed throughout my career," he wrote.
The beauty pageant drew backlash earlier this month after its Thailand director Nawat Itsaragrisil publicly berated Miss Mexico, Fatima Bosch, at a pre-pageant event for not posting promotional content on her social media platforms.
In videos that have since gone viral, Ms Bosch and several other contestants could be seen walking out of the event, and some could be heard shouting at Mr Nawat.
Mr Nawat later claimed that some of his words were misunderstood - but his conduct nevertheless prompted a stern rebuke from the Miss Universe Organisation, which has since sent a delegation of international executives to take over running the competition.