The middle order batsman was ordered to return home from England by the team management with the approval of the board after he failed to clear two fitness tests in Birmingham where the Pakistan squad has set up its conditioning camp for the Champions Trophy.
The national selectors have already sent batsman, Haris Sohail, to replace Umar in the Champions Trophy squad which plays its first match on June 4 against India at Birmingham.
"We will be holding a full inquiry into the affair and to confirm what happened. We want to know how Umar was cleared fit to be sent to England where he failed two fitness tests," he said.
"It's a matter of concern for us. We will investigate this matter to fix responsibility. We have to see if Umar really got unfit after reaching England or his test taken in Pakistan had flaws," Khan said.
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Khan insisted that the board after consultation with the head coach and selectors decided there would be zero tolerance on having unfit players in the side.
They are also unhappy with reports from England that the team management didn't treat Umar properly in Birmingham after the fitness tests and he was made to sit on a bench and not take part in any practice and told to return home.
"There is a strong feeling that even if Umar was not 100 percent fit and with 10 days remaining before the first match instead of sending him back the team support staff which includes a trainer and physio should have worked on the fitness of Umar and got him ready for the tournament," one source said.
Umar had also been dropped for the tour to the West Indies two months back after failing fitness tests.