PCB chairman Shaharyar Khan has confirmed that he had met Waqar yesterday and apologised to him.
"Waqar might not have been able to produce desired results with the national team but he remains one of our top players and has big status in cricket. It was unfortunate that his confidential report was leaked to the media from the board," Shaharyar said.
"I apologised to Waqar and wished him the best after he informed me and had decided to resign as head coach. But the meeting was held in a good environment and I have promised him the board will hold an inquiry to find out how a confidential report was leaked," he said.
"But apparently it was conveyed to Waqar that the board has decided to act on the recommendations of the fact-finding committee and hunt for a new coach," one source said.
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He said Waqar then decided to resign himself although he lost out on a compensation payment of around 4.8 million rupees which the board would have paid him if they had sacked him before the completion of his contract period.
Waqar said he would have resigned later but after the leakage of his report he wanted to make a point and get the board officials to listen to him.
"I have said it if they want they can also use the dues payable to me (around six million rupees) now for improving the domestic cricket structure. At the end of the day it is all about improving things in Pakistan cricket and not about individuals," Waqar added.
"You can't be successful every time. I know I couldn't deliver what the nation expected of me. But to me what hurt is that Najam Sethi, who initially appointed and backed me, didn't bother to take my calls after the World Cup 2015 when I wanted some reforms to be made in the team and selection policy," he said.