Greece began processing 530 newly arrived migrants on Piraeus on Monday and the coastguard rescued hundreds more from the sea over the weekend, as popular resistance against the arrivals grows.
The new arrivals come as Greece is stepping up efforts to build new registration centres for refugees. The so-called hotspots are being set up in EU border zones to help process a rush of people trying to enter Europe.
Greece has seen an outsize number of new arrivals in the last year - even if many of them quickly attempt to move on to richer, northern European countries - and has come under EU criticism for not doing enough to hold back the surge.
One hotspot has now been completed on the island of Lesbos, with four more planned by the end of February on the islands of Chios, Samos, Leros and Kos. Many migrants first arrive on Greek islands after attempting a crossing from Turkey.
However, the centres have become the target of protests by residents. Those on the islands are worried that the centres will deter tourists from visiting. Those on the mainland are concerned that the numbers of arrivals will grow out of control.
An estimated 68,023 people travelled from the Turkish coast to Greek islands from the beginning of 2016 to February 6, according to the UN High Commissioner for Refugees at the weekend.
Monday saw renewed protests on Kos and in Piraeus and Thessaloniki. In Thessaloniki, demonstrators blocked the entrance to a former military barracks that is to be converted to housing for 4,000 refugees.
In Piraeus, right-leaning protesters from the Keratsini district protested plans to build a new centre there. A counter-demonstration was planned.
Separately, authorities reported the rescue of 573 migrants from the Aegean Sea during the weekend. A coastguard officer told dpa it was "very lucky" that no one drowned.