"It turned out to be a booby-trapped device that may have been alive," the spokeswoman said. It was defused by a police mine clearance expert.
Police then evacuated the Zlicin store and another at Cerny Most, an eastern suburb, as a precaution.
The latest scare comes after a string of small explosions at European Ikea stores.
On June 10, a blast in the kitchen equipment department of a store in Dresden, Germany, reportedly left two customers needing hospital treatment, while booby-trapped alarm clocks blew up at Ikea stores in Belgium, France and the Netherlands on May 30, but caused no damage or injuries.
No one has so far claimed responsibility for the explosions.
Ikea has four stores in the Czech Republic, two in Prague, one in Brno 200 kilometres (125 miles) southeast of the capital, and a fourth in Ostrava some 350 kilometres east of Prague.