Pakistani media last week reported that Afridi and Waqar did not get on during the 3-2 one-day series win against the West Indies.
Afridi, not happy with selection matters, on his return home early on Sunday lashed out at Waqar.
"Although the differences with the coach are not such which could not be solved... I must say that everyone should do his job and need not interfere in other's work," Afridi told reporters.
Afridi said he will soon meet Pakistan Cricket Board (PCB) chairman Ijaz Butt to take up the matter before giving further details to the media.
With a relatively young string, Pakistan won the first three matches comfortably before going down in the last two matches against the West Indies who were also depleted by the non-selection of senior players like Chris Gayle, Ramnaresh Sarwan and Shivnarine Chanderpaaul.
Afridi regretted his team lost a good chance to win all the matches.
"We should have clean sweeped the West Indies but the defeat in the last two matches left a bad taste in the mouth, we flopped in batting and that's why I must say we need a batting coach," said Afridi, who admitted he was also below par in the series.
"I played average cricket because I was tired after the World Cup and only played the series on the advice of some friends and former players."
