The UN High Commissioner for Refugees Jennifer Pagonis has been given until May 22 to make a submission to a Senate committee dealing with the draft legislation tabled on Friday.
Ms Patagonis said if the boatpeople do not receive the same high standards as those onshore in Australia, they could effectively be discriminated against.
The UNHCR said the legislation looks similar to a controversial policy first implemented by the Australian government to deal with the arrival in 2001 of a group of boatpeople rescued by the Norwegian container ship Tampa.
Ms Patagonis said the offshore processing is likely to take place on Nauru, a country which is not a party to the 1951 Refugee Convention.
The UNHCR has also called for guarantees to ensure that families are not split up or turned away without proper consideration.