Yekaterina Geniyeva, president of Soros's Open Society Institute, said the attackers took away all of its documents in the climax to a long-running commercial dispute.
She told a radio station on Friday the men identified themselves as working for the Sektor-1 company, which says it owns the city centre building.
"The most terrifying thing was that they took away all our documents. We do not know where," she said, adding the foundation did not recognise Sektor-1's ownership rights.
Oil billionaire arrest
She said she did not think there was any direct link between the incident and the arrest of oil billionaire Mikhail Khodorkovsky, which some fear may herald a state crackdown on big business.
But she said there might be "some connection".
Geniyeva said the men broke a pane of glass and ushered out guards and foundation employees in the Thursday night raid. Police did not interfere.
1930 - Born in Hungary
1952- Graduates from London School of Economics
1956- Moves to USA
1987 - Sets up Soros Foundation-Soviet Union
1992 - Helps bring down the sterling
1997 - Accused of trying to wreck Malaysia's economy
Kantemir Karamzin, head of Sektor-1, said Soros's foundation had to leave the building as it had failed to pay the rent.
A Hungarian-born American, Soros is no stranger to controversy.
He is widely known as the man who broke the British pound in 1992, after helping force sterling out of Europe's exchange rate mechanism.
Soros was also reportedly the first American to earn a billion dollars in a single year.
His institute aims to promote a civil society in post-communist Russia, and he has poured millions of dollars into philanthropic works in Eastern Europe.
However, he has sharply criticised the recent jailing of Yukos chief executive Mikhail Khodorkovsky.
He also 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".