Fayemi alleged that some of his fellow governorship aspirants disrupted the election because he was leading.
The primary was allegedly disrupted by thugs loyal to other candidates, Babafemi Ojudu, a former senator, and Bimbo Daramola, an ex-member of the house of representatives among others.
The aspirants had alleged that Fayemi, who was said to be leading in the election, compromised the process, sparking protest among delegates which eventually became violent.
Reacting to the incident, Fayemi berated Ojudu and Daramola, describing them as being "too desperate".
A statement issued on Sunday, May 6, by Fayemi's media aide, Yinka Oyebode, quoted the minister as saying that APC does not deserve the ridicule it was subjected to at the primary.
Fayemi noted that the security operatives had been informed of plans by some aspirants to deploy thugs to disrupt the election.
According to him, the security agencies noted the information and promised to beef up security at the venue.
He said, "It is quite painful seeing some desperate elements trying so much to rubbish the party we all laboured to build to national reckoning, out of share lust for power.
"If the quest for political position is to serve, then one wonders why the desperation being displayed by the likes of Femi Ojudu and Bimbo Daramola.
"Certainly the conduct of these desperate aspirants falls short of the minimum standards expected of anyone that professes progressive ideals. We urge our teeming supporters and loyal party members not to be discouraged by this despicable act. This surely shall pass, and better days are ahead. Our collective rescue mission has indeed begun.
It was gathered that the hoodlums broke the ballot boxes while chorusing hate songs in Yoruba against Fayemi.