Senior batsman Mohammad Hafeez was accused of hiding his knee injury from the team management as per the report.
According to excerpts of the report leaked in the media today, Waqar said that Afridi appeared non-serious and not concerned about the team's performance in the two events.
He claimed that Afridi had regularly missed practice sessions and meetings.
The rift between the head coach and captain is not new as the two had also clashed during Waqar's first tenure in 2011 as a result of which the cricket board Afridi as ODI and T20 captain.
The legendary pacer expressed his "disappointment" at the report being leaked to the media.
"I am totally disappointed and upset with the way the report has been leaked and I think the Pakistan Cricket Board needs to find out who leaked it and for what purpose," Waqar told PTI from Lahore.
"I can only say what I have written in the report is what I sincerely feel. It is now up to the board to decide what to do. Because I have said before cosmetic measures will not bring about any good in Pakistan cricket," Waqar added.
He claimed that he had requested the national selection committee to include Salman Butt in the squad for the Asia Cup and World T20, but chief selector Haroon Rasheed, without consulting him, included Khurrum Manzoor in the side.
Waqar also accused his former teammate Moin Khan of promoting the culture of favoritism in the dressing room when he was the chief selector, saying that he even gave gifts to some players and them out regularly during the 2015 World Cup, which affected the team spirit.
Waqar also blasted the Pakistan Cricket Board (PCB) officials for the leakage of his confidential report and their refusal to meet him at the Gaddafi stadium.
"Is this the way to treat someone. I went to the PCB offices today to meet with Shaharyar Khan (chairman) and Najam Sethi. I wanted to ask them how and why this report was leaked and who is playing this dirty game and trying to paint me as the villain," a visibly upset and angry Waqar said.
"They didn't have the courtesy to even meet me. I was sitting three rooms away from their offices. But they just told me on phone they are busy and can't meet me today," he said.
"I want to know the purpose of leaking this report. Specific parts are being aired in the media to defame me and show me as the villain. What I have said in totality is not being shown. I went to the chairman's residence and gave this report and told him to study it in detail. Yet it was leaked," Waqar added.
Waqar said nothing would improve in Pakistan cricket unless sincere steps were taken.
"For years we have seen Pakistan cricket decline and it hurts me a lot. I don't care about my job whether they keep me or not. I would now appeal to the Prime Minister to take serious notice and do something to stop this rot," he said.
The Pakistan coach said it was time to bring in an outsider and new faces who don't carry extra baggage.
"We must bring in an outsider, someone who doesn't have to listen to anyone or take calls and pressure from influential people in team matters," Waqar said.
Waqar said he had served Pakistan cricket for years and the Gaddafi stadium was a second home to him.
"But frankly speaking I am now fed up. I am trying to do something good for Pakistan cricket and these games are being played with me like always."
PCB chairman Shaharyar Khan later told the media that he was in a high-level meeting and had told Waqar he would meet him tomorrow.
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