The Swedish company said meatballs would still be available to buy in its stores and only one batch was being withdrawn as a precaution until further tests on it could be done.
A spokesman said internal tests had shown no problems up to now.
He said in a statement: "Ikea takes the test result from the Czech Republic authorities showing indications of traces of horse meat seriously.
"The concerned production batch of meatballs has been withdrawn from the Swedish Food Market in the Ikea stores.
"Already two weeks ago, Ikea Group initiated DNA analyses of all meat products in the range. Twelve tested samples of different batches of meatballs showed no traces of horse meat.
"To validate the test results, we are now initiating further tests on the same production batch in which the Czech Republic authorities found indications of horse meat."
A spokesman said they were expecting test results in the coming days and will then be able to give more information.
He said: "Ikea is committed to serving and selling high quality food that is safe, healthy and produced with care for the environment and the people who produce it.
"We do not tolerate any other ingredients than the ones stipulated in our recipes or specifications, secured through set standards, certifications and product analysis by accredited laboratories."
The firm said it had issued "a sales stop" of the concerned batch in Slovakia, the Czech Republic, Hungary, France, Portugal, Italy, Netherlands, Belgium, Spain, Greece, Cyprus, Ireland as well as the UK.
The company said the move was out of concern for "potential worries among our customers", adding its own controls had not shown any traces of horse.
It was not clear if Ikea would also stop selling meatballs in other countries
The horse meatballs were labelled as beef and pork and were in one-kilo frozen packs sent to the Czech Republic for sale in Ikea stores there.
A total of 760 kilos (1,675lbs ) of the meatballs were stopped from reaching the shelves.
Ikea's furniture stores feature restaurants and also sell typical Swedish food, including the Kottbullar meatballs.
The Czechs also found horsemeat in beef burgers imported from Poland during random tests of food products.
Meanwhile EU agriculture ministers met in Brussels to discuss the widening scandal's fallout, with some member states pressing for tougher rules to regain consumer confidence.
They must agree on binding origin disclosures for food product ingredients, starting with a better labelling of meat products, German agriculture minister Ilse Aigner said.
"Consumers have every right to the greatest-possible transparency," she insisted.
She backs the German initiative; but others like Ireland say existing rules are sufficient although Europe-wide controls must be strengthened to address the problem of fraudulent labelling.
The scandal has created a split between nations like Britain who see further rules as a protectionist hindrance of free trade under the bloc's single market, and those calling for tougher regulation.