Stoltenberg's comments came as he attended a meeting of EU foreign and defence ministers which was set to approve the bloc's plan for a naval operation to tackle people smugglers operating mainly out of Libya.
"First of all this is a human tragedy, people are losing their lives trying to cross the Mediterranean," Stoltenberg said when asked about reports the Islamic State group was trying to smuggle fighters into Europe by hiding them on migrant boats.
"And this underlines the importance that we have to respond to this turmoil."
Western officials often use the term foreign fighters to describe people from Europe and the Middle East who have travelled to fight with IS in Iraq and Syria.
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Stoltenberg cited NATO's own efforts to work with countries in North Africa and the Middle East to tackle the root causes of the migrant problem.
But he stressed that the US-led military alliance was not for the moment taking part in the EU's unprecedented naval mission, which follows a series of deadly shipwrecks of migrant boats in the Mediterranean.