"It came two days ago from Austria," Alexeyenko told AFP. "The shipment is over 20 tonnes," he said, adding that the enterprise that supplied the meat had been struck off the list of suppliers.
The contaminated meat will either be destroyed or returned to the supplier, he added.
Horse meat is a traditional delicacy in Russia and can be found in many restaurants and stores across the country.
Alexeyenko said the problem with the contaminated meat was that it was not clear what it was made of.
"We are talking about adulterated meat products containing horse meat," he said. "The source of this meat is unknown," he noted, adding that old ill animals could have been used to make it.