Andrei Gorkov, head of investments at Rosnano, a holding company specialising in nanotechnologies, was arrested after he bought a plane ticket to leave the country, the committee said.
It has opened a case on claims of "abuse of authority", saying Gorkov transferred funds regularly between 2011 and 2013 to an account held by a bank that went under and was closed by the authorities in late 2014.
The bank's failure cost Rosnano about 738 million rubles (11.6 million euros, USD 12.9 million at current rates).
Rosnano is led by Anatoly Chubais, an economist who oversaw liberal market reforms in the 1990s after the fall of the Soviet Union, including a privatisation drive, a role for which he remains highly criticised by many in Russia.