Haroon, 20, was told by the International Boxing Association (AIBA) that he cannot box for Pakistan.
"Pakistan boxing federation got an email that Haroon can't represent them as he represented England as a youth," Shah told BBC Radio Manchester.
"We have sent letters to AIBA and we're hoping that they'll accept our request."
Haroon, younger brother of WBA Super and IBF Light Welterweight Champion Amir Khan, was due to represent Pakistan in the upcoming World Boxing Championships in Azerbaijan, which act as a qualifier to the Olympics.
Haroon, who represented England as a youth in 2009, initially hoped to box for England in 2010 Delhi Commonwealth Games, but after being overlooked, opted instead to fight for Pakistan, and won a bronze medal.
"Their (AIBA) rulings say that when a boxer becomes a national of more than one country, he has to decide which country he wants to represent," Shah said.
After becoming a Pakistani national in 2010, Haroon decided to represent Pakistan. Shah said that "he decided he wanted to box for Pakistan, which he did in Commonwealth games, where he won a bronze medal.”
“If you go by that rule, he did decide to box for Pakistan and so he should be entitled to box for Pakistan in the future as well,” Shah added.
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Biased decision.