Camouflage-clad men have forced staff to leave the Moscow offices of the Open Society Institute founded by the US billionaire George Soros.
George Soros: Campaigning for rule of law in eastern Europe
At least 30 men stormed the offices and seized computers and documents in the raid, which began late on Thursday, the foundation's lawyer Pavel Kuzmin said.
Mr Soros' senior policy adviser Laura Silber told BBC News Online that the foundation had responded by filing criminal charges.
She said the 100 staff were locked out and "it is impossible to work in Russia now".
A Moscow firm called Sector-1 which owns the building said it acted because of a rent row.
But the institute's Moscow chief said the raid could be related to the crackdown on Russian oil giant Yukos.
Yekaterina Geniyeva, who is currently outside Russia, was quoted as saying she could see "a certain connection" with the Yukos affair.
Mr Soros, whose institute aims to promote a civil society in post-communist Russia, sharply criticised the recent jailing of Yukos chief executive Mikhail Khodorkovsky.
On Tuesday he warned that Russia "may now be entering a phase of state capitalism, where all the owners of capital realise that they are dependent on the state".
His comments came in an interview with the weekly Moskovskiye Novosti, recently acquired by Mr Khodorkovsky.
He denounced the 25 October arrest of the oil tycoon as "persecution".
The foundation's lawyer said two lorry-loads of documents and equipment were driven away and the foundation had no access to its server and files.
Ms Silber said the foundation had no temporary premises in Moscow.
"We're in the clear over legal occupancy of the building, with full legal rights," she said, adding that the lease was valid until 2009.
An important Aids prevention programme funded by the Soros institute is now jeopardised, she said.
The Open Society Institute has been working in Moscow since 1987 and has spent nearly $1bn in Russia.