He added that such measures would only serve to trigger "widespread anxiety and anger,” which may be used by terrorists as propaganda.
"Blind measures, not based on solid intelligence, tend to be ineffective as they risk being bypassed by what are today sophisticated global terrorist movements," he added.
In the statement, Guterres refrained from directly referring to Trump or his policies, but voiced his concerns over measures being taken around the globe which were endangering the safety of refugees.
"This is against the fundamental principles and values on which our societies are based," he said.
UN High Commissioner for Human Rights Zeid Ra’ad Zeid al-Hussein delivers a speech at the opening of a new Council's session on June 13, 2016 in Geneva.
UN High Commissioner for Human Rights Zeid Ra’ad Zeid al-Hussein has also condemned the ban, stressing that it was illegal and "mean-spirited," while noting that "discrimination on nationality alone is forbidden under human rights law."
On Monday, Human Rights Watch urged Guterres to denounce the ban. "At a time when governments, civil society and business leaders are increasingly speaking out, it´s important that the UN´s message not come solely from the UN human rights chief," said the rights group’s deputy director for global advocacy Philippe Bolopion.
"Secretary General Guterres should take a clear stand that Trump´s executive order is a blow to refugees, reflects bigotry and will do little to address terrorism," he added.
Trump issued an executive order late Friday to impose a 90-day entry ban on citizens from Iran, Iraq, Syria, Yemen, Sudan, Libya and Somalia, block refugees from Syria indefinitely, and suspend all refugee admissions for 120 days.