A NATO fighter guarding its nervous northern states accidentally fired a secret air-to-air missile near the border with Russia yesterday. They still can't find it.

The Spanish Eurofighter Typhoon was policing the border of Estonia to deter Russian incursions, and keeping an eye on their activity over the Baltic Sea.

While taking part in a routine training manoeuvre over the southeast Estonian town of Pangodi, the Typhoon accidentally triggered an AMRAAM — an advanced medium range air-to-air missile. It was engaged in a mock dogfight involving another Spanish Typhoon and two French Mirage 2000 fighters.

It was an area 100km from Russia's border. But the missile is capable of flying between 75km and 120km. It carries an explosive warhead.

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The missile's final trajectory is not known.

The advanced missile, filled with sensitive software and sensors, has a self-destruct facility for such incidents. But NATO isn't sure this activated.

It may be sitting on the ground somewhere.

Estonian authorities have initiated an urgent search for the weapon, and appealed for anyone who may have seen it to step forward. Military helicopters and emergency services have been called in on the hunt.

Missile systems for the BAE Systems Typhoon at the Farnborough Airshow in Farnborough, England. Photo / Getty Images
Missile systems for the BAE Systems Typhoon at the Farnborough Airshow in Farnborough, England. Photo / Getty Images

The Spanish Defence Ministry has initiated an investigation.

"A Spanish Eurofighter based in Lithuania accidentally fired a missile without causing any harm," it said in a statement. "The air-to-air missile has not hit any aircraft. The defence ministry has opened an investigation to clarify the exact cause of the incident."

It has issued a warning through the Estonian defence department stating hat people should avoid approaching "something that looks like a missile".

Estonian Prime Minister Juri Ratas took to Facebook, saying the accident was "extremely regrettable" and "thank God no human casualties".

Similar military exercises have been temporarily suspended.

"I am sure that the Estonian defence forces will, in co-operation with our allies, identify all the circumstances of the case and make every effort to make sure that nothing like this happens again," he said.

Firing a modern missile is no simple task. It's not like accidentally pulling the trigger on a gun. The missile must be activated. Data must be fed into its on-board computer. Its sensors must be given a target.

But pilots are given a 'snapshot' option — for use when the fighter is in the thick of a dogfight with no time to spare for niceties. It can be fired in the general direction of a target before its sensors activate to establish a 'lock-on'.

Even this, however, requires the pilot to deliberately trigger that mode.