Aegean Airlines has laid on special flights to evacuate residents and visitors as multiple earthquakes threatened Santorini.
At least 9,000 people out of a population of 15,500 are reported to have left the island since Sunday after hundreds of earthquakes were recorded nearby.
While outside the tourist season, the majority of those leaving are locals.
Hundreds of people queued at a port in the early hours of Tuesday morning to board a ferry leaving for the mainland.
Aegean operated five special flights to Athens on Monday in addition to four regular scheduled services, carrying a total of 1,294 passengers.
Eight Airbus A230 flights ran on Tuesday offering 1,400 seats and at least two extra flights to the Greek capital are being deployed today (Wednesday).
The airline said on Tuesday: “Within the first two days, about 2,500-2,700 passengers are estimated to have been carried from Santorini to Athens with our flights.
“Due to the special circumstances, the aircraft arrive in Santorini with very few passengers, mainly government officials, while the flights departing from Santorini at almost full capacity.
“Should extreme circumstances prevail, additional special flights are to be operated on Wednesday.”
Schools in Santorini and 12 other islands in the Aegean had been shut and people advised by the Greek civil protection ministry against large indoor gatherings.
Most of the strongest earthquakes are originating from an area around the tiny islet of Anydros, northeast of Santorini.
Scientists are on alert for Santorini and the nearby islands of Amorgos, Anafi and Ios as seismic activity remains intense in the region.