Afridi was stripped of the captaincy on the eve of this weekend's two one-day internationals against Ireland in Belfast after allegedly claiming interference from Pakistan Cricket Board officials in team selection.
The all-rounder is due to face a meeting with the PCB to explain his comments, although the governing body have denied his demotion came as a result of them.
Afridi was widely lauded after leading Pakistan to the semi-finals of the World Cup in March but, after pulling out of the Ireland series to be with his sick father, question marks remain around his future role with the national side.
"I have got no idea about that. It is the Cricket Board's decision what they want to do about the captaincy," Waqar said.
"My job is to look after the team and to deliver the goods.
"It's tough to say anything about it."
Waqar also denied reports he had fallen out with Afridi, after claims the all-rounder had also been unhappy with his role with the team.
"It was the papers that made all this," he added. "There is nothing in it."
Waqar was more concerned with his team's preparations ahead of Saturday's opening match against an Ireland team he is wary of following their World Cup exploits.
Waqar pointed to Ireland's stunning success over England on the sub-continent as reason to be on guard as he aims to maintain his side's motivation for a series that has followed hot on the heels of a tour of the Caribbean.
"They are a good side. They are young, they are very enthusiastic," he added.
"They chased 300-plus against England. Who thought they could do that?
"They are a very positive side and they are big fighters. We have to play really well."
Waqar is also fearful of literally being caught cold by the Irish after his side flew in from the balmy temperatures in the West Indies on Thursday.
"Coming from 35-40 degrees with a lot of humidity there and coming into this weather it is hard to adjust, especially with all those flights as well," added Waqar, who also pledged to play a full-strength team.
"I think we are professional enough to adapt to the conditions very quickly.
"We know what Ireland are capable of. They are a very tough opponent. We have to be very, very careful."
The Pakistan coach also backed calls, led by the Irish, for the International Cricket Council to backtrack on their decision not to include associate nations at the next World Cup in Australia.
The ICC's chief executive committee is due to discuss the possibility of introducing a qualification process at a meeting in Hong Kong next month.
Waqar believes Ireland would be fully deserving if a decision was made to allow them a route back into the 2015 World Cup.
"Just looking at the last World Cup, because I haven't seen much of their cricket outside that, but there they played like champions. It was top-level cricket," he said.
"The ICC have got a different ruling but I personally believe they have a good side and they are getting better day by day."
