Spanish Typhoon jets regularly patrol the skies above Lithuania, Estonia and Latvia as part of NATO's Baltic Air Policing mission.
But it hasn't been confirmed whether the procedure was actually triggered and authorities haven't ruled out the possibility the missile landed on the ground.
The incident happened on Tuesday afternoon "in an area of southwest Estonia authorised for this type of exercise", the ministry said.
As the Estonian Air Force continued to search for the missing weapon, the public were warned not to look for it themselves.
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Estonian Prime Minister Juri Ratas said on Facebook that there were "thank God no human casualties", and called the incident "extremely regrettable".
He said the Estonian Defence Forces were working with its allies to ensure it did not happen again.
The Spanish Defense Ministry also opened an investigation. The Spanish Eurofighter detachment comprised of six jets.
The Spanish Defense Ministry said it was investigating the incident and said the missile did not hit any aircraft or "cause any harm".
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Spain led the BAP mission in 2006 and 2016 and augmented it out of Ämari in 2015 and 2017, making this the fifth tour to the Baltics. It began on May 1 and will conclude on August 31.
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