Shaharyar said an MRI scan proved that Shoaib had no bruising and the player not taking the field in the crucial Test match was a "very serious matter."
"I need an inquiry because the MRI showed that there was no bruising. The doctor himself felt there was no bruising, that the side was all right, he had an injury in his wrist.
But then not to go out to field, just to buck up the boys, I think was below par," the PCB chief said in an interview to BBC World's 'Hard Talk Pakistan' programme to be telecast on Wednesday.
"But we need to have a medical inquiry in order to establish whether what we see is correct or not. I am not going to condemn any one, especially a senior player like Shoaib. When he says that I have a bad side and I can't bowl, I can't field, [then] I have to take his word at face value," he said.
Shaharyar said it was the responsibility of every player to give his best even if he was injured.
"Every player has a responsibility. Every player must go out and buck up the rest of his players, even if he is injured. And therefore, if a player says I am not going out, it's a very serious matter. And it was at a time when he (Shoaib) had taken three wickets, we needed him on the field, we needed to have a go at the Indians. But unfortunately, he said he was not going out on the field. Now, I think that's a very serious matter," Shaharyar said.
Asked who is responsible for the defeat, he conceded: "We're all to blame. But I think basically, the players have to get together and ask themselves -- why did they allow themselves to be rolled over in that way, why did they give up so early, what happened?
"I am going to have an inquiry on why Shoaib was not functioning. All right, he couldn't bowl, but he could have gone on to the field. The next day he batted with abandon."
Referring to the third Test at Rawalpindi, where Pakistan surrendered meekly in the second innings to lose the match by an innings and 131 runs, Shaharyar said any player found not giving his best for the country would have no place in the team.
"In the last innings, there was acceptance of defeat much too early. There wasn't a playing for the honour of the country, none of the feeling of 'over my dead body', except one player, Asim Kamal, who was badly injured."