The arrest of Evgeny Adamov, who was the head of Minatom in 1998-2001, is certainly quite an embarrassment for his former ministry. The exact nature of the charges is not clear at the moment, but they reportedly include embezzlement of about $9 million of the funds that DoE was sending to Russia to improve security of its nuclear sites.
Rosatom immediately announced that the charges have nothing to do with the period when Adamov was the head of the ministry. Quite possible. However, the many private companies Adamov was involved in had quite close connections with Minatom. So, if Adamov is extradited to the United States and the investigation goes forward, we may hear interesting details about Minatom's inner workings.