Vitaly Lopota, president of Energia, is suspected of approving unauthorised loans to an international space consortium, Russia's equivalent of the FBI said in a statement.
Lopota is one of the country's most important space officials, responsible for a company that has won the bulk of the contracts for Russian space hardware.
Since the retirement of the US shuttle, the Soyuz rocket-and-capsule system is the sole means for sending humans into space, responsible for transporting astronauts to the International Space Station.
Sea Launch is an international service which launches rockets from a mobile sea platform. It has faced severe financial problems.
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The money should have gone towards the manufacture of spaceships in line with international agreements, and the terms of the loans were also not beneficial for Energia, the Investigating Committee said.
It said this had resulted in losses for the state, which partly owns Energia, of 41 million rubles ($1.14 million).
Energia traces its history back to the very dawn of Soviet spaceflight efforts in 1946 after World War II and was behind the launch of the first satellite and man into space.
Its full name is the Sergei Korolyov Rocket and Space Corporation Energia, named after the great Soviet rocket designer seen as the genius behind Yuri Gagarin's first manned spaceflight in 1961.