While Shakib is free to play competitive cricket from September 15, BCB's ban on NOCs (No Objection Certificate) for overseas leagues is valid till end of 2015.
"Clearly for Champions League Twenty20 he is not available to us," Venky Mysore, the Knight Riders' chief executive told ESPN Cricinfo.
"Although we have the options it is unfortunate considering he is an important player for us. We just have to respect the BCB's decision," Mysore told the website.
Shakib played a key role during KKR's successful campaign in the last edition of IPL, scoring 227 runs at a strike rate of 149.34 and taking 11 wickets with an economy rate of 6.68.

Dhaka: Bangladesh all-rounder Shakib Al Hasan's six-month ban imposed last month for "misbehaviour" has been lifted, the Bangladesh Cricket Board said on Tuesday.

"After Sept. 15, Shakib will be available for selection," BCB president Nazmul Hassan told reporters after a board meeting.
However, the embargo on participating in overseas competitions will stand.
Bangladesh's most prominent cricketer was banned for what the BCB called a "severe attitude problem".
He later apologised and made a passionate public plea to the board to reduce the punishment.
Shakib, who has played 34 tests and 136 one-day-internationals, was accused of travelling to the West Indies to play in the Caribbean Premier League Twenty20 tournament without clearance from his board and was subsequently ordered to return to Bangladesh.
The 27-year-old had reportedly threatened to quit playing for his country and had an altercation with coach Chandika Hathurusinghe. Shakib has denied the allegation.
Tuesday's decision paved the way for Shakib to play in the home series against Zimbabwe in October-November and the Asian Games kicking off on Sept. 19.
"The Board acknowledged that the player had demonstrated exemplary behaviour since he was handed the penalty and we have been pleased with the manner of his appeal," Hassan said.
"The Board will continue to monitor him once he returns to playing cricket. We hope that he has had the opportunity to reflect on a difficult phase in his life and will come back as the player the world knows and the personality everyone expects him to be," he said.

Latest News from Sports News Desk