Shakib is reportedly facing a six-month ban following a host of recent disputes.
There were suggestions the all-rounder had threatened to quit the international game after he was asked by coach Chandika Hathurusingha to return from Caribbean Premier League duty and attend a Bangladesh training camp.
A defiant Shakib denied those allegations, claiming there had been a misunderstanding over a No-Objection Certificate (NOC) clearing him to play in overseas competitions.
However, the 27-year-old has now been punished for what BCB president Nazmul Hasan described as "serious misbehaviour", with Shakib having also been involved in an alleged altercation with a spectator during a one-day international with India last month.
"He has a severe attitude problem, which is unprecedented in the history of Bangladesh cricket," Hasan told reporters following a board of directors meeting in Dhaka on Monday.
"We think that his behaviour is such that it's directly impacting the team.
"This morning he [Shakib] called me. He thought that he had the NOC. He did not have any.
"He admitted that he misbehaved with the coach. He apologised for the misbehaviour.
"We want to give a clear message: if it is repeated, he might be banned for life. There will be no compromise when it comes to discipline."
A talented batsman and spin bowler, Shakib made his debut for Bangladesh in 2006 at the age of 19.
He has gone on to represent his country in 34 Tests, 136 one-day internationals and 35 Twenty20s.