Oleg Frolov and two other suspects are accused of a "large-scale fraud", said a statement from the Russian investigative committee, which handles major criminal investigations.
"Frolov, using his official position, took part in a criminal conspiracy with two other co-conspirators," said the statement.
"In the course of the execution of the contract, they stole budgeted funds during the purchase of equipment."
Frolov would be held in custody pending his trial, the statement added.
Roscosmos, once a source of national pride, has for years been suffering financial problems and has been hit by a series of corruption scandals and embarrassing technical failures such as the loss in August of the Luna-25 probe.
Russia is nevertheless still planning its own space station, to replace its aging section of the International Space Station (ISS), and a revival of its moon programme.
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