"What we have seen is that the intense Russian air strikes mainly targeting opposition groups in Syria are undermining the efforts to find a political solution to the conflict," Stoltenberg said as he arrived for talks in Amsterdam with EU defence ministers.
Syrian peace talks in Geneva earlier this week broke up acrimoniously as long-time Moscow ally President Bashar al-Assad launched a fresh offensive against rebel forces in Aleppo with massive Russian backing.
The UN Security Council is due to meet later today to discuss the situation, with the negotiations on hold until February 25.
Stoltenberg said NATO strongly supported efforts to end the war in Syria, which has cost more than 250,000 lives and displaced half the population, many of them fleeing to Europe in its worst migrant crisis since World War II.
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He said the air strikes and Moscow's military build-up in Syria and the eastern Mediterranean were a challenge for the US-led alliance and especially for key member Turkey, whose airspace Russian planes have violated.
"This creates risks and heightens tensions and is of course a challenge for NATO," he added.
Turkey shot down a Russian fighter jet along its Syrian border in late November and the two sides have been engaged in a bitter war of words since.