Around 200 arrive smoothly as part of deal aimed at stemming crisis but rights fears persist over future asylum seekers.
The European Union’s top migration official says deportations will intensify after the first group of refugees were returned to Turkey from Greece this week.
EU Migration Commissioner Dimitris Avramopoulos told a news conference on Wednesday the expulsions were just beginning and the numbers were still “very low”.
“But it’s better to start working slowly. I believe in the course of time we will scale up… It’s a good start,” he said.
Avramopoulos was in Turkey’s capital Ankara earlier this week to demand the country introduce legal protections for asylum-seekers before the EU began sending them back.
The Greek diplomat said that was still indispensable for larger-scale returns to start.
Reports recently surfaced that Turkey had been rounding up and expelling Syrian refugees back to their war-torn country, allegations that Ankara has denied.
Three days after the deportation order came into force, new arrivals on the Greek islands from Turkey dropped to 68 in the 24 hours to Wednesday morning from 225 the previous day, data from the Greek migration ministry showed.
Visiting the Finnish capital Helsinki on Wednesday, Turkish Prime Minister Ahmet Davutoglu said the agreement “is functioning and the [number of] illegal migrants is in decline”.
Al Jazeera’s Harry Fawcett, reporting from the coast of Badem in Turkey, said refugees were still making attempts to cross the Aegean Sea.
According to reports, large-scale deportations from Greece could restart as early as Friday. But Nikos Xydakis, junior foreign minister for European affairs, hinted there could be a two-week “lag” because of a last-minute flurry of asylum applications by refugees who are trying to avoid expulsion.
“We knew there would be a lag, an intermediate period before the programme takes off, of at least two weeks to get through the first batch of applications,” Xydakis told reporters.
He nevertheless said the next set of expulsions would likely take place “from Friday onwards”, without going into further detail.
In an interview with Al Jazeera, Leo Dobbs of the UN refugee agency, said “mechanisms were not in place” for Greece to deal with the refugee influx.
Last Monday, at least 202 refugees were sent back to Turkey from Greece.
Under the terms of the EU-Turkey deal, all “irregular migrants” arriving on the Greek islands from Turkey since March 20 face being sent back, although the accord calls for each case to be examined individually.
And for every Syrian refugee returned, another Syrian refugee will be resettled from Turkey to the EU, with numbers capped at 72,000.
On Wednesday, the European Union’s executive put forward options to spread refugees more evenly across member states, but Central European member states have resisted such efforts.