Announcing plans for an inquiry into the series defeat -- the first ever suffered by a Pakistani team to India on home soil -- Khan said on Sunday he was shocked at the way Pakistan had collapsed in the decider.
India wrapped up a remarkable victory in Rawalpindi on Friday, clinching a 2-1 series triumph by an innings and 131 runs.
But the manner of Pakistan's capitulation has angererd (PCB) chief Khan, who accused the home team of caving in without a fight.
"Obvious flaws in Pakistans performance will be addressed in a calm and professional manner and I have taken serious notice of this lack of commitment to national honour," Khan said in a statement.
The role of pace bowler Shoaib Akhtar is certain to come under scrutiny.
Akhtar, who only claimed seven wickets in the series, did not bowl for a major part of India's innings after suffering a back injury.
The fact however that Akhtar subsequently went on to bat without any obvious signs of discomfort has fuelled rumours of a bust-up between the bowler and his skipper Inzamam ul-Haq.
Inzamam accused Akhtar of letting the team down in the wake of the third Test defeat.
Khan said a medical commission would be set up to assess the true extent of Akhtar's injury -- and he made it clear that any indication Akhtar had been malingering would be severely punished.
"I will be wanting to interview each potentially offending player to inquire the reasons for not upholding team morale and national honor.
"I want to make it crystal clear that any player who is found incapable or unwilling to give 150 per cent for team morale and national honour will have no place in the Pakistan team," he said.
"My main concern for the present is the manner in which the Rawalpindi Test was lost without the semblance of a fight.
"While some players, like the courageous Asim Kamal clearly demonstrated fighting spirit there were others who patently failed the test by their carefree, unprofessional approach in Pakistan's second innings," said Khan.
"I have decided to set up a medical inquiry committee to report on Akhtar's injury as also the large number of injured players who have depleted and undermined Pakistan's cricketing strength."
The inquiry committee headed by a senior orthopaedic consultant will be formed by PCB chief executive officer Ramiz Raja and it will submit its report in a week.