The labour action comes at the tail-end of Europe's summer holiday season, and extra pre-strike ferries were called into action on Sunday to move people at the last minute.
A top Greek court has ruled that asylum-seekers newly arriving on Greek islands from Turkey should no longer be held there while their applications are assessed, court officials said on Wednesday.
Winter could bring death to asylum seekers stranded on crowded Greek islands with only summer tents for shelter, aid groups said on Wednesday, urging a mass relocation to the mainland.
A total of 1,662 migrants have landed on Greek islands near Turkey since a landmark EU-Turkish deal on curbing the influx took effect on Sunday, a Greek coordination panel said.
A plan to return all irregular migrants arriving on Greek islands back to Turkey could take effect on Sunday if EU leaders strike a deal with the Turkish prime minister, senior EU officials said.