The Czech State Veterinary Administration reported its findings to the European Union's Rapid Alert System for Food and Feed.
The inspectors took samples for DNA tests in IKEA's unit in the city of Brno from a product labelled as "beef and pork meatballs", a statement said.
It added that the consignment of meatballs that was tested had not been distributed to consumers.
A spokesman for the institute said he did not know whether the meatballs were distributed in other European countries.
IKEA said they were made by a single Swedish supplier.
The Czech veterinary authority said it detected horsemeat in meatballs labelled as containing beef and pork imported to the country by Sweden's furniture retailer IKEA.
The State Veterinary Administration said the one-kilogram packs of the frozen meat balls were made in Sweden to be sold in IKEA stores.
A total of 760 kilograms of the meat balls were stopped from reaching the shelves in the Czech Republic.
Czech inspectors have found horsemeat in meatballs made in Sweden for the furniture retailer IKEA group, the Czech news agency CTK reported.
Ikea said it "deeply regrets" use of forced prison labour by suppliers in communist East Germany.