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The decision to freeze the majority of shares in the company came days after Yukos chief executive Mikhail Khodorkovsky was arrested at gunpoint by special forces operatives at a Siberian airport and charged with fraud and tax evasion.
Russia's general prosecutor's office confirmed last night that it had seized shares from two companies - one registered on the Isle of Man and the other on Cyprus.
Alexander Shadrin, a Yukos spokesman, said: "I can confirm that a controlling stake of 61% of shares has been seized, although these shares still retain voting and dividend rights."
Yukos had just offered shareholders a record $US2 billion dividend sweetener in an effort to steady the beleaguered firm after shares closed almost 12% down after the seizure. Yukos shares have fallen more than 30% from their all-time high of $16 on 17 October.
The government attack on the company has been seen by many as a power play within the political structure as Kremlin hard-liners attempt to strengthen their influence over President Putin and reassert state authority over businesses.
Another victim of the crisis has been Putin's chief of staff, Alexander Voloshin, a leader of another pro-business group, who resigned after in protest over Khodorkovsky's arrest.
The appointment of Voloshin's successor, to one of the most powerful jobs in the Kremlin, is now seen as a signal of Putin's commitment to reforms.
A choice of one of the many administration officials linked to the state security apparatus is likely to be taken as a bad sign for reform prospects.