Misbah fell awkwardly while chasing a shot in the third over of New Zealand’s innings during the second day-night international in Sharjah.
New Zealand won the match by four wickets to level the five-match series at 1-1. Pakistan won the first match by three wickets in Dubai on Monday.
Waqar said Misbah remains doubtful for the third match, also in Sharjah on Sunday.
“Misbah has a hamstring issue and he will have a scan and then we will decide. He is not very good,” said Waqar.
Asked who would lead the team if Misbah is ruled out, Waqar said it would be up to Pakistan Cricket Board chairman Shaharyar Khan to decide.
“Look, captaincy’s issue is chairman’s domain and we will probably ring him if Misbah is not available to decide what we are going to do,” said Waqar.
All-rounder Shahid Afridi is one likely choice.
Fast bowler Bilawal Bhatti was also ruled out of the third one-day after he injured his right hand during practice and needed stitches.
Another fast bowler, Umar Gul, is also on the injury list after missing the second game due to a sore ankle.
“It’s a long tour and there are bound to be injuries, we have lost Junaid (Khan) and we need to solve these injury issues before the World Cup next year,” said Waqar.
Pakistan has been in United Arab Emirates since October. They played a Twenty20, three one-day internationals and two Tests against Australia before their two Tests, two Twenty20 and five one-day series against New Zealand.
Junaid injured his knee during the one-day series against Australia in October and is still recovering.
Waqar said he was still searching for a right bowling combination, badly affected by the suspension of ace spinner Saeed Ajmal and all-rounder Mohammad Hafeez due to illegal bowling action.
“We are trying to build the right combination for the World Cup and these issues have not allowed us to do so,” said Waqar, who blamed a below par total for the defeat on Friday.
“I guess we couldn’t get the target we were looking for, things would have been different had we got some more runs,” said Waqar of Pakistan’s 252 all out.
New Zealand chased down the target in 46 overs with skipper Kane Williamson hitting an unbeaten 70.
“We didn’t bowl right line and length and that failed us.”
The fourth and fifth matches will be played in Abu Dhabi on Wednesday and Friday. -AFP