Guterres' speech in the Japanese capital to an audience of diplomats, NGOs and university students came as European countries are increasingly inclined towards tightening immigration rules in the worst refugee crisis the continent has faced since World War II.
"The idea that Europe can announce the closure of borders to Muslim refugees or reject Muslim refugees is only an argument that will suit perfectly Daesh in its campaigns against Europe," Guterres said, using another name for IS.
"It's necessary to look at the complexity of the security situation and understand that the problem does not come from refugee movements," he added.
Concerns about security have increased further since IS attackers killed 130 people in Paris this month in the worst such violence on French soil.
The November 13 attacks have stirred fears in Europe and North America that jihadists could try to blend in with refugees to gain entry to Europe or the US and strike later.
A former Portuguese prime minister, Guterres reiterated comments made Wednesday that the Paris attacks cannot be blamed on refugees, stressing that the perpetrators were "home-grown".
"It is always possible for a terrorist organisation to try to infiltrate a (refugee) movement that is not properly controlled," he said.
Guterres, the UN High Commissioner for Refugees who is due to complete his 10-year tenure at the year-end, added: "Refugees are the victims of terrorism, and the refugee movements are the consequence of terrorism."
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