The arrest of Uralkali chief executive Vladislav Baumgertner followed the break-up of a joint venture between Moscow and Minsk which rocked the £13 billion global potash mineral salt market and upset Belarus.
"It is impermissible to detain a person on his way home after he came for talks at the invitation of the Belarusian government," said indignant Russian Deputy Foreign Minister Grigory Karasin.
He warned Belarus that the executive's arrest could affect diplomatic relations between the countries.
Belarusian investigators said earlier on Tuesday that Mr Baumgertner would be held for two months.
He was arrested at Minsk airport on Monday on suspicion of abusing his position over Uralkali's decision to quit the joint Russian-Belarus cartel.
He faces up to 10 years in jail if convicted.