While the overcrowded and unsanitary official centers were the target of strong criticism, their closure has left a gap.
However with Greece in the grip of its most severe economic crisis since World War Two and facing an uncertain future while talks over yet another international bailout begin, prospects of immediate relief appear distant.
"It's a huge problem because there are families with young children in a really bad situation with no water, with no food," Kanakis said, adding that his organisation tried to provide basic medical care but more was needed.
"We need a place, a center where they can stay," he said.
Along with Italy, which has faced a massive influx of African migrants arriving by boat from Libya, Greece is at the front lines of a crisis that has threatened to overwhelm public services already worn down by years of recession.
According to figures from the United Nations High Commissioner for Refugees, migrant arrivals in Greece have leapt almost tenfold in the first six months of the year, jumping from 3,452 in the first six months of 2014 to 31,037 this year.
A coordinated response from Europe has been slow in coming however, caught up by wrangling over how to distribute the arrivals among countries where anti-immigration parties have seen a steady rise in support.
"This is an emergency for Europe not to tell that they will help, to help. Otherwise, the situation will become worse and worse and we will see in the middle of Athens pictures that the humanitarian doctors have seen back in the east or back in Africa," Kanakis said.