Danish F-16 jets were scrambled around noon on Tuesday to address unidentified objects nearing Baltic air space.
The Estonian Defense Force did not reveal what the two fighter jets identified, but Air Force chief Colonel Jaak Tarien said the jets reacted quickly and the staff of the air force base acted professionally.
The unidentified aircraft are thought to have been Russian.
Four Danish fighters arrived in Estonia on May 1, turning Ämari into the Baltic's second airbase in the region. The fighters, and 60-strong ground crew, will stay in Estonia until the end of August, and are likely to be replaced by jets from another NATO air force.