Waqar quit last month citing health problems and Alam has been made director in the PCB, changes which paved the way for Afridi's return.
Waqar said he was happy with Afridi's decision but called the whole episode "disappointing".
"To retire from cricket was his decision and now coming back to cricket is also his own," said Waqar.
"I had said this before and I say this again, if he had some differences with me he should have sat down and sorted out those differences."
When he retired, the PCB suspended Afridi's central contract and revoked permission for him to play abroad. Afridi then went to court, but the dispute was resolved after a private meeting with Butt.
Afridi appeared before a PCB disciplinary committee and was fined $53,000 but his permission to play abroad was reinstated.
Afridi, who will link up with the Melbourne Renegades in the new Big Bash League starting in December, said he was in peak physical condition.
"I have been playing regular cricket and want to play the one-day series against Sri Lanka as I am in good shape and have been working hard on my batting and bowling," he said.
Pakistan is playing Sri Lanka in the first of three tests, which began in Abu Dhabi on Tuesday. They will also play five one-days and a Twenty20 during the series, relocated to the United Arab Emirates over security fears.
Pakistan captain Misbah-ul Haq last month said he was ready to welcome Afridi back to the team.
"First he has to make a decision over his retirement, then the matter will go to the PCB and only after that I can decide. He has been playing well and has enough cricket left in him," he said.
-AAP