Two government officials told Reuters the government was concerned about the deal because Nebius's activities were funded by Yandex.
A third, separate source said Nebius is part of Yandex's Dutch holding company, Yandex NV, and would be part of the new international company post-restructuring.
"They were basically told that as long as they're connected to a Russian company, it's not going to work," one of the sources told Reuters.
"Our Dutch holding company is in the process of divesting its Russian business – unfortunately this isn't a fast process," Shtan said.
Energy issued a statement last month saying neither the company nor its chief executive, Michael Bobrov, has any connection with Russia.