Three German combat squadrons reported full operational readiness to NATO at 9:10 am (0710 GMT) on Friday.
With the weapon systems and about 250 soldiers, the German Air Force is taking over protection against ballistic missiles, but also against aircraft and cruise missiles.
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The alliance is thus taking account of the heightened security situation, without there being any concrete indications of an attack.
The PATRIOT air defence systems launchers are stationed at Vilnius airport, which is about 160 kilometres from the Russian exclave of Kaliningrad and 30 kilometres from Belarus.
The two-day NATO summit begins on Tuesday.