The Human Rights Law Centre says Australia's plan to resettle refugees in the US could leave hundreds languishing in detention on Nauru and Manus Island.
The Australian government says 1,600 refugees it has detained offshore for three years are eligible for resettlement in the US.
But the centre's head of legal advocacy, Daniel Webb, said there was no plan for the refugees the US leaves behind.
"This has been a pretty dark chapter in our history. It only ends and the government only gets to pat itself on the back when each and every person who is currently suffering at their hands on Nauru and Manus is rebuilding their lives in safety."
Mr Webb said the resettlement deal could lead to the deportation of 370 refugees from Australia including 40 children who were born there.
"It also says nothing about whether families separated by the current offshore detention arrangements will ever be reunited," he said.
The United Nations Refugee Agency, refugee advocates and refugees themselves said the deal could leave families divided and maroon some asylum seekers on the islands forever.
Under the deal announced on Sunday by the Australian Prime Minister, Malcolm Turnbull, the resettlement would be co-ordinated by the UN Refugee Agency.
The Agency's Canberra office said in a statement, however, that while it endorsed the agreement it was not a party to the deal.
"The arrangement reflects a much-needed solution for refugees who have been held for over three years and who remain in a precarious situation. Appropriate solutions must be found for all of them. Australia must be part of the solution for refugees and asylum seekers who have family ties to Australia."
The Refugee Action Coalition's Ian Rintoul said there was a danger President Donald Trump could back out of the arrangement when he is innaugurated in January.
Mr Rintoul said even if the deal went ahead, the priority it gave to resettling families, women and children meant hundreds of single men could be left behind.
"What is very clear is that this is not an all encompassing deal. This is something which has been done in haste, it's been done by a desperate government I think probably driven by the change of administration in the United States," said Mr Rintoul.
"It is absurd that the Australian government is not willing to provide protection to people who have come here by boat but is willing to go to the United States and other countries to see whether it can."
The Manus Island detainee and Kurdish Iranian journalist, Behrouz Boochani, also doubts President Trump will honour the deal.
Mr Boochani said he was not willing to leave Manus until Australia was made to answer for his wrongful three-year detention
"If they want to transfer me to America it's hard for me to accept because of justice. They tortured me, how can I accept that, they tortured me for a long time. I will stay here and I will resist. I want to say, no, you don't have respect for human rights and show to people that there is not any justice."
Malcolm Turnbull, on the other hand, is confident President Trump will honour the deal.
"The United States has no closer ally, we have no closer ally. So we have a very long history of cooperation with the United States in matters of this kind where we are able to pursue our mutual and our respective humanitarian and indeed national security objectives."
Mr Turnbull said US officials would visit Australia and Nauru later in the week to begin vetting the refugees.