Bangladesh Cricket Board (BCB) president Nazmul Hassan said the board had unanimously decided to suspend the 27-year-old from "all kinds of competitive cricket" for the next six months, ruling him out of Bangladesh's tour of the West Indies in August.
He will also be barred from playing in any cricket leagues abroad until December next year, the president said.
"He has a severe attitude problem, which is unprecedented in the history of Bangladesh cricket," Hassan told reporters.
"We think that his behaviour is such that it's directly impacting the team."
The suspension came as Shakib reportedly threatened to quit international cricket after he was called back to Dhaka before a planned appearance in the Caribbean Premier League (CPL) Twenty20 tournament.
Hassan said Shakib was travelling to the Caribbean without any clearance from the BCB, and had also "misbehaved" with coach Chandika Hathurusinghe. He gave no further details.
"This morning he called me. He thought that he had the NOC (no objection certificate). He did not have any. He admitted that he misbehaved with the coach. He apologised for the misbehaviour," Hassan said.
"Shakib is our role model. He is like an ambassador," the president added. But he said the player did not care about others, and "I think we cannot tolerate it anymore."
Shakib, who for years has been the world's leading all-rounder and is one of Bangladesh's finest cricketers, could not be contacted for comment.
Hassan said the player had a history of disciplinary problems, and was banned for three matches in February for an indecent gesture to local fans. The ban kept him out of key Asia Cup matches.
Last month he beat up a spectator after the latter reportedly used abusive language against his wife during a Bangladesh-India match.
"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," Hassan said of the latest apparent incident.
On Sunday, Shakib returned to Dhaka and denied that he had made any threat to quit international cricket. "I want to play cricket for another ten years," he said.
Shakib made his international debut in 2007 and has been the most consistent performer for Bangladesh.
He has played 34 Tests scoring 2,278 runs with a batting average of 37.96 and taken 122 wickets, the country's highest. He has played 134 one-day internationals scoring 3,835 runs and scalping 171 wickets.
A left-handed batsman and a slow left-arm bowler, Shakib held the International Cricket Council's top all-rounder position for years.
Shakib also helped Kolkata Knight Riders become champions in the Indian Premier League (IPL) twice and has featured in English county cricket.
He played all eight games for Barbados Tridents in the inaugural season of the CPL last year, ending up as the second highest wicket-taker in the competition.
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