"We regret the impact that the implementation will have on asylum seekers," UN refugee agency spokesperson Andrej Mahecic told reporters in Geneva.
The Supreme Court ruled earlier this week that Trump administration restrictions preventing most Central American migrants from applying for asylum at the US border could temporarily take effect while lower court proceedings play out.
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The decision, which stayed a lower court's temporary injunction, will be in effect while a broader case against the policy plays out in the courts.
The policy declares ineligible for asylum any migrants who enter the United States from the southern border and who have not asked for asylum protection in any of the countries they crossed to get to there.
While the Supreme Court ruling is only temporary, Mahecic voiced concern over the impact implementing the Trump policy could have on people seeking protection while the case winds its way through the courts.
He stressed that "any person fleeing violence or persecution must be able to access full and effective asylum procedures and international protection."
Asylum requests at the southern US border are often made by families and unaccompanied children saying they have fled endemic violence and poverty in their countries, and Mahecic insisted that many are "in urgent need of safe haven".
"It is imperative that those people be identified quickly and afforded the safety and assistance that they need, including the right to seek asylum," he said.
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Mahecic pointed out that the Supreme Court had not yet addressed the "substance of the policy in question".
"We trust that the US courts will make the final determination on the merit of the case that reflects consciousness of the protection risks involved," he said.
The policy in question is among a host of measures Trump has taken in a bid to stem the flow of migrants, including the deployment of troops at the southern border.
Official statistics show the number of people apprehended or declared inadmissible at the southern border has dropped to around 64,000 in August, from more than 144,000 in May.
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