The alliance gave the go-ahead for the flights on Monday, a NATO spokesman told journalists.
“All Awacs reconnaissance flights will take place solely over Alliance territory,” the official said.
It comes as Russia cements its control of Ukraine’s Crimea ahead of Sunday’s referendum to join Russia. Ukraine and the West say this is illegal.
In the latest move on Monday, armed men – said to be Russian troops and local militias – seized a military hospital in Crimea.
The attackers marched into the hospital in the regional capital Simferopol, threatening staff and some 30 patients.
Pro-Russian troops are also blockading Ukrainian troops across Crimea.
Moscow has officially denied that its troops are taking part in the blockades, describing the armed men with no insignia as Crimea’s “self-defence” forces.
The government in Kiev – as well as the US and EU – accuse Russia of invading Ukraine, in violation of international law.