"We must act immediately on the ground...we must coordinate our efforts to be more effective," he said during a visit to the island.
Lesbos is on the front line of a migration crisis the likes of which Europe has not experienced since the aftermath of World War II.
More than 650,000 migrants and refugees, have reached the Greek islands so far in 2015 using the eastern Mediterranean route, the International Organisation for Migration (IOM) said earlier this month.
Of those, over 500 died, including many children.
Rights groups have repeatedly criticised Greek authorities for being unable to provide adequate shelter to migrants and refugees on Lesbos and other islands.
Amnesty International last week said "small children and families were left exposed" as winter approaches.
In addition, countries along the migrant route through the Balkans have begun tightening restrictions by accepting only those fleeing war, causing a backlog of hundreds of people Thursday on the Greek-Macedonian border.
AFP reporters said 2,000 people were gathered at the Greek-Macedonia border waiting to cross.
"Some are ready to build fences, some are ready to help 24/24 to help these people", Andriukaitis said on Lesbos, after witnessing volunteers helping migrants land on the rocky beach of Skala Sykamineas, in the north of the island.
EU health chief says resources urgently needed on Greek island
20 November 2015
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European Health Commissioner Vytenis Andriukaitis on Thursday said resources were urgently needed on the Greek island of Lesbos where hundreds of migrants continue to land daily from neighbouring Turkey.
