According to Turkish authorities, the Russian SU-30 warplane breached Turkish airspace for hundreds of metres in the district of Yayladagi in Hatay province for two minutes at 12:10 pm on October 3, but returned to Syrian airspace after one warning.
However, Russia has denied the allegations. It said it was due to poor weather and navigation error, BBC reported.
Turkey has twice summoned the Russian ambassador - once over the first violation which occurred on October 3, and then over a second violation that took place on October 4.
Stoltenberg said Russia had not provided "any real explanation" for the violation, which "lasted for a long time."
He called the violation "unacceptable" and said Nato was taking it "very seriously".
The Nato head also said there had been "a substantial military build-up" by Russia in Syria, including ground troops and naval capabilities.
Russia's deployment was of "great concern", he said, calling on Moscow to avoid further escalating tensions with Nato.
Russia's air campaign in Syria began on September 30.