"The continuing increase in anti-migrant and anti-refugee rhetoric and violent attacks against these communities... across all Europe is deeply worrying," Ban told a press conference in The Hague.
"These actions in divided communities sow instability and betray the values and human rights standards that underpin international solidarity."
Europe is currently grappling with its worst migrant crisis since World War II. Over one million people crossed clandestinely from Turkey to Greece in 2015 and more than 150,000 have made the trip since the start of this year.
Earlier, Ban held talks with Dutch Foreign Minister Bert Koenders on the migrant issue as well as the war in Syria and other topics.
"We need open, honest and constructive dialogue to avoid all the polarisation," Ban told reporters after his talks with Koenders, who travelled to west Africa at the weekend for talks on stemming the flow of economic migrants.
Any "solution requires increased political will to address the root causes of migration in the countries of origin," the UN secretary general said.
"Current policies are clearly not adequate," he insisted, saying "a global response" was need to address conflicts as well as human rights abuses.
But the EU-sanctioned deportations have drawn sharp criticism from rights groups.
More than 50,000 people have been stranded in Greece since the closure of Balkans migrant route in February, with around 10,000 stuck in a slum-like camp on the Macedonian border, which has seen a growing number of violent incidents.
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