Shahid Afridi had yesterday quit T20 team's captaincy due to their poor performance at the prestigious event, where they managed just one win at the Group stage.
They lost to top teams including arch-rivals India, New Zealand and Australia while managed just one win against Bangladesh.
"I am resigning from my post today with a heavy heart," Waqar, who took over as coach in 2014 for the second time , told reporters. Incidentally, a day earlier, Waqar had said that he does not want to bow out being painted a "villain".
The 44-year-old, who first coached the side in 2010-11, wants his recommendations to be implemented by the Pakistan Cricket Board.
"I want my recommendations to be implemented. They were not acted on when I first made them in 2015."
A part of his report to the PCB was leaked to media. He had criticised the Pakistan Cricket Board's decision to not give him a say in the selection process and also questioned the leadership style of Afridi.
"We lost to New Zealand, Asia Cup and the World T20 due to poor captaincy. Over several occasions, I had made it clear that Shahid Afridi was not performing with the bat, ball or as a captain but I was not listened to," he said.
"I had made a lot of recommendations after the 2015 World Cup, including sending some boys back to first-class cricket for at least a season so that they can regain their hunger for the game and re-think their approach and attitude to play for Pakistan, but no recommendation was implemented."