Nikolai Tsiskaridze, 39, who has been at the Bolshoi since 1992, is one of the theatre top talents.
He sparked conflict when he accused bosses of using the attack on Sergei Filin to conduct a witch hunt against him.
A spokeswoman said Nikolai Tsiskaridze, would leave at the end of the month.
“I can confirm that yesterday Tsiskaridze was given notice that his fixed-term contracts will not be renewed. His contract runs out June 30,” Katerina Novikova told Rossiya 24 on Saturday.
Katerina Novikova refused to give a reason for the decision.
In an NTV television interview on Sunday, Nikolai Tsiskaridze questioned the theatre’s right to let him go.
“To be honest, this is still not clear, because I’m on staff as a ballet artiste,” he said.
“When I was taken on, I joined the staff. I didn’t sign any paper to be released from this. It’s all very confusing.”
Earlier this year, the Bolshoi filed two reprimands against Nikolai Tsiskaridze for giving unauthorized interviews after the attack on Sergei Filin in January.
Under Russian law, multiple reprimands can be grounds for dismissal.
Nikolai Tsiskaridze appealed and a Moscow court annulled one of the reprimands.
In his outspoken interviews, Nikolai Tsiskaridze complained of corruption and called for the theatre’s entire management to be sacked and for himself to be put in charge.
It led to a tit-for-tat response from Bolshoi director Anatoly Iksanov, who suggested Nikolai Tsiskaridze might have played a role in inciting the attack on Sergei Filin, which left him with severe burns to his face and fighting to save his sight.
Nikolai Tsiskaridze has denied having anything to do with the attack and insists the Bolshoi has been trying to drive him out.
Soloist Pavel Dmitrichenko and two alleged accomplices have been charged in connection with the attack and are in jail awaiting trial.
In March, Pavel Dmitrichenko admitted to discussing the attack but denied ordering the use of acid.
They face up to 12 years in prison if convicted.
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