His foundation was declared a "foreign agent" by the Russian justice ministry in October, making it subject to more checks.
Thursday's raid came ÀÌÅ¿øºÎµ¿»ê a day after Mr Navalny condemned the forcible conscription of one of his allies to serve at a military base in the Arctic.
In a video recording made during the search in Moscow, he said officers from Russia's bailiffs service were seizing "everything".
CCTV footage shows the door of the foundation being cut open with power tools.