A company official told Reuters the investigators had taken more than 50 boxes of documents.
Yukos must pay $3.4 billion in back taxes for 2000 by August 30. The oil giant says it cannot do so as it is banned from selling assets to raise money, while it can generate only $1.7 billion by the deadline.
Claims for 2000 have already been upheld by courts, while a similar $3.4 billion claim for 2001 has yet to be ruled on by them. Yukos has said this week investigators were also checking its 2002 accounts.
Analysts say Yukos, whose shares fell three percent on the news, may end up being presented a total of $10-$15 billion in back taxes for 2000-2003.
The state has threatened to dismantle the firm by selling its core Siberian oil units to cover the back tax bill. It hired investment bank Dresdner Kleinwort Wasserstein to value Yugansk, Yukos's main Siberian oil producing unit.