Greece has adopted a tougher stance on migration since the conservative government led by Prime Minister Kyriakos Mitsotakis came to power in July.
Mitsotakis told his EU counterparts last week that the union must review asylum rules and warned economic migrants that they will be returned to Turkey if they are not entitled to asylum, government spokesman Stelios Petsas said on Tuesday.
"If they give their money to traffickers hoping to permanently cross into Europe, they will only lose it," Petsas told reporters. "Even if they reach Greece, since they are not entitled to asylum, they will return to Turkey."
"They can no longer come to Greece and apply for asylum hoping that they stay here forever, as it was the case with the previous government," Petsas said, referring to former prime minister Alexis Tsipras' left-led administration.
More than 12,000 people arrived in Greece in September, the highest level in the three-and-a-half years since the EU agreed a deal with Turkey to seal the Aegean corridor to Europe.
Athens has announced plans to deport 10,000 people who do not qualify for asylum by the end of next year.
Logothetis said up to 300 more people would be leaving Samos this week, and up to 2,000 from all outlying islands next week. Greece aims to move up to 20,000 off the islands by the end of the year, he said.