The PCB was forced to issue an explanation that Bilawal was stopped at the airport from entering the UAE because he had travelled on an expired visa.
"He travelled on a expired visa which he had earlier used to go to Dubai while returning from South Africa," an official said.
The official said arrangements had been made to lodge Bilawal at a hotel at the airport and a new visa had been applied for which should be available soon.
"He inadvertently used his UAE visa to enter Dubai on his way back to Pakistan from South Africa on Tuesday," another official said.
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But some former players and critics questioned the working of the board.
"Isn't the board's officials dealing with travel and logistics of the team supposed to check these things before the team leaves on a tour and what about the team management, didn't they see he had an expired visa?" former Test player Rashid Latif said.
Bilawal made his debut for Pakistan in the recent series against South Africa leaving an impact with his bowling and batting.
Pakistan is due to play a one-off T20 international against Afghanistan on Sunday in Sharjah before it hosts Sri Lanka on a 10-match tour from next Wednesday.