Greece was processing 530 newly arrived migrants in Piraeus on Monday, after the coastguard rescued hundreds from the Aegean Sea and as pressure on Athens to deal with the crisis grew from both inside and out.
The people - many fleeing conflict in Syria, Afghanistan and Iraq - arrived from Turkey amid growing hostility from Greeks and as Macedonia, the next country on their path, began reinforcing the border against trespassers.
Greece has stepped up efforts to build new registration centres for refugees, in line with demands from EU partners. The so-called hotspots are being set up in EU border zones to help process a rush of people trying to enter the bloc.
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.
After processing in Greece, virtually all migrants want to continue north, most of all to Germany, to seek asylum.
Last year, around 1 million people traversed the Balkan route, from Turkey, across Greece, Macedonia, Serbia, Croatia and Slovenia. Smaller numbers went through Bulgaria or Hungary.
Countries north of Greece narrowed the gates in November, allowing only Syrians, Iraqis and Afghans to continue. It is, however, believed that others continue moving north by sneaking across borders.
Macedonia has begun extending the existing barricade at its border with Greece - a fence reinforced with razor wire - to a total length of 37 kilometres. The army began construction work on Monday, the daily Vecer reported.
Greece is a part of the EU and its passport-free Schengen zone; Macedonia is not. Nonetheless, western officials have been proposing to fortify Macedonia's border against migrants if Greece fails to gain control over the flow arriving from Turkey.
A vocal proponent of the idea, Austrian Foreign Minister Sebastian Kurz, on Monday arrived in Bosnia, launching a six-country tour of non-EU Balkan states, expected to be dominated by migration-related issues.