The incident happened when Akmal, captaining the Punjab province against Sindh in Rawalpindi was asked about his team combination.
Akmal first informed that all-rounder Nasir Nazir would be playing in place of left-arm pacer Junaid.
"I just found out when I walked into the ground that he [Junaid Khan] is absent. I am very surprised. The manager and coach told me he is not going to be playing today. It's a shocking news for me as a captain," Akmal said.
"I am very disappointed to hear about what Umar Akmal has said just now giving the impression I ran away from this match. The fact is I am dealing with a case of food poisoning and I had informed the team management about this and they were aware of this fact and the team doctor advised me rest," Junaid said.
The PCB said its inquiry committee headed by General Manager (Domestic Cricket Affairs) Shafiq Ahmed would look into the matter and submit a report and if necessary disciplinary action can be taken.