Testing showed in addition to pork meat "horse DNA, chicken DNA and cattle DNA", the food safety watchdog Rosselkhoznadzor said in a statement on its website.
It did not say in which store the investigators found the mince.
Auchan in Russia did not immediately respond to a request for comment from AFP.
In 2013, the revelation that horsemeat was being sold as beef in ready foods in stores across Europe shocked consumers and led to the introduction of harsher checks.
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Horsemeat is not a huge taboo in Russia, where it is eaten as a delicacy by some minority groups.
The latest checks on Auchan came after Rosselkhoznadzor recently upbraided the company several times over food hygiene.
On July 30, it alleged that Auchan was adding extra days to the best-before dates on chilled meat products in its distribution warehouses in the Moscow region.
A day later, the agency published a photo of a pizza in an Auchan store in the Moscow region saying the pepperoni was past its sell-by date.
Russian President Vladimir Putin in June extended an embargo on most food imports from Western countries that had slapped sanctions on Moscow over the Ukraine crisis.