"The hijacker has just been arrested," Cypriot government spokesman Nicos Christodoulides said on Twitter, without providing further details.
A man emerged from the aircraft and then walked across the tarmac and raised his hands to two awaiting counter-terrorism police officers, an AFP correspondent reported.
They laid him on the ground and searched him for around two minutes before taking him away.
The hijacker had claimed to be wearing an explosives belt when he took over the plane.
Police had yet to enter the aircraft 30 minutes after his surrender.