The agency criticised the level of protection available to those sent to Manus Island under the new government plan in a two-page letter of assessment released today.
"UNHCR's assessment, based on recent visits to PNG, is that there are currently significant shortcomings in the legal framework for receiving and processing asylum seekers from Australia," the agency said.
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"These include a lack of national capacity and expertise in processing, and poor physical conditions within open-ended, mandatory and arbitrary detention settings.
"This can be harmful to the physical and psycho-social well-being of transferees, particularly children and family."
The agency acknowledged that some of these issues were "being addressed", but noted its concern over the prospect of further transfers taking place under the new arrangement.
Immigration Minister Tony Burke visited the Manus Island facility this week after SBS's Dateline program broke allegations of rape and torture among asylum seekers being held there.
"In terms of making sure that the standards are there - that people have been given the opportunities for recreation, that people are being treated with dignity [and] with the proper welfare supports that is around them - what I saw today is in line with most of the principles I want," he said.
More than half of around 130 asylum seekers on Manus Island have been taken to Australia as the new policy takes shape. It's expected new arrivals will be settled at the centre within two weeks.
