"The composition of a Spanish squad deployed in Lithuania, jets and crews will not be changed until the end of their mission," the spokesperson said.
The ministry pointed out that the flight plan of the forces deployed in Lithuania was determined by NATO, not Spain.
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The spokesperson noted that it was too early to speak about causes of the incident in Estonian airspace.
"An investigation into the causes of this incident has been launched. The probe is underway and there are no preliminary results [of the investigation]," the ministry added.
On Tuesday evening, a Eurofighter Typhoon 2000 fighter jet belonging to the Spanish Air Force mistakenly fired an air-to-air missile while flying over Estonia.
Baltic Air Policing Mission aims at ensuring the safety of the airspace over Estonia, Latvia and Lithuania. The mission was launched in 2004, when the three states joined NATO. As the Baltic states do not have jets that could carry out air policing, NATO members' jets stationed in Lithuania, including Eurofighter Typhoon 2000, control their airspace on a rotational basis.