"I call on Russia to act responsibly and to fully respect NATO airspace. Russia must take all necessary measures to ensure that such violations do not happen again," Stoltenberg said in a statement.
"Previous incidents have shown how dangerous such behaviour is," he said.
In November, Turkey shot down a Russian fighter jet on the Syrian border, sparking a war of words with Russia which insisted its plane had not violated Turkish airspace.
Russia launched a massive air campaign in September against rebels fighting to overthrow Syrian President Bashar al-Assad, a long-time Moscow ally who Turkey bitterly opposes.
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At the same time, he made absolutely clear that NATO would stand by Turkey, the second largest military power in the alliance after the United States.
"NATO stands in solidarity with Turkey and supports the territorial integrity of our ally, Turkey."
He recalled that the 28-nation alliance had agreed in December to help bolster Turkey's defences with the deployment of AWACS early warning and surveillance aircraft but added the caveat that this decision predated the latest incident.
Ankara called in the Russian ambassador yesterday "to strongly protest and condemn" the latest alleged violation of its airspace.