"We confirm that the court has decided to disqualify Dudley for two years and will appeal this decision," the spokesperson said, adding that Dudley would remain the CEO at least until the appeal had been heard.
The company said the Presnensky Court of Moscow was acting on an application from the state labor regulator.
Labor inspectors said Wednesday the move had been initiated by Viktor Vekselberg, one of the four major Russian shareholders of TNK-BP, who have repeatedly called for Dudley's dismissal.
TNK-BP is split 50-50 between BP and its Russian billionaire partners, who have been battling over management and strategy at the joint venture, which is Russia's third largest oil producer and accounts for a quarter of BP's overall output.
Last Friday, the Presnensky Court fined Dudley $21 for administrative violations.
Dudley, who has been unable to have his Russian visa renewed, is running TNK-BP from abroad. His whereabouts have not been disclosed.
TNK-BP's Russian shareholders accuse Dudley of acting only in BP's interests. The British oil major said the Russian investors want to seize control of the company.