Fayose said the violence at the first APC primary in the state is an indication that Fayemi is not wanted in Ekiti.
A mobile policeman had allegedly fired a gunshot at Fayemi, who escaped it, but the bullet hit former House of Representatives member, Opeyemi Bamidele and two others.
The incident occurred at the state APC Secretariat in Ado-Ekiti, the state capital, as Fayemi's campaign train was about to take off.
The shooter has been arrested and the police said they are investigating the alleged attack.
Fayose, however, blamed Fayemi for the incident, saying his "desperation" brought "bloodshed" to the state.
The outgoing governor made the comment via his Twitter account on Friday.
"Fayemi is having all these challenges because of his desperation. It is instructive that there was chaos at the APC primary election and his return to Ekiti today brought bloodshed to a once peaceful Ekiti State. Those whom the gods want to destroy, they first make mad," he wrote.
Fayose had earlier boasted that his incumbent deputy, Professor Kolapo Olusola, who is the PDP candidate in the July 14, 2018 governorship election in the state, will beat Fayemi of the APC by a wide margin.
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On May 30, Fayemi, a one-time governor of the state, resigned his position as Minister of Solid Minerals Development to pursue his gubernatorial ambition.