Uralkali and its Belarusian partner had accounted for up to 40 percent of global trade in potash, a key ingredient in fertilizer.
The Russian company pulled out of the trading venture in July, accusing the Belarusian government of allowing state-owned Belaruskali to export potash independently. Because most of the venture's employees reportedly went to work for Uralkali, Belarus was left with virtually no qualified staff to manage its potash exports. That raised fears that Uralkali was trying to gain control over Belarus' resources and start a pricing war.
Belarus responded by arresting Baumgertner, also on suspicion of abuse of power. But on Friday, Belarusian President Alexander Lukashenko announced that the executive now faces charges of embezzlement, not abuse of power. If convicted, he could face 12 years in prison.
If charged in Russia with abuse of power, Baumgertner could face up to four years in prison.
Belarusian authorities have also issued an arrest warrant for Russian billionaire Suleyman Kerimov, who is Uralkali's biggest shareholder.
In Monday's statement, the Investigative Committee said it was also looking into whether a former Belaruskali executive, Konstantin Solodovnikov, had abused his powers.