Australia says the UN refugee agency is part of a deal to send refugees to the United States who Canberra currently has in its care in Papua New Guinea and Nauru.
The Australian immigration minister Peter Dutton made the statement on Channel Ten TV after the UNHCR said it was not part of the bilateral arrangement.
Mr Dutton however said the UNHCR is front and centre to the arrangement, which he said is also a requirement from the US.
He said the agreement, which was announced by Australia at the weekend, provided for the US to take people that have been found to be refugees by the UNHCR.
The processing of the asylum seekers has been done by Australia.
The UNHCR said earlier while it endorsed the agreement it was not a party to the deal.