The Sri Lankan asylum seekers were rescued at sea by the Australian Customs ship before being taken to Indonesia's Bintan Island, where they refused to disembark for a month.
The Federal Government says it will now be up to the UN agency to determine where the refugees should be settled.
Opposition immigration spokesman Scott Morrison says he thinks the deal which was struck to get the asylum seekers to leave the ship will ensure them of an automatic trip to Australia.
"Australia does its fair share in terms of taking refugees who've been determined as such by the UNHCR in Indonesia but there is no rule that says we always take every last one of them," he said.
"But what I suspect will happen here is that the special deal that the Prime Minister did with the Oceanic Viking will follow through and they will have got their quick run to Australia.
"That sends a very obvious message to people smugglers operating in the area."
The Greens' Sarah Hanson-Young has welcomed the UN's decision to declare the asylum seekers refugees.
"It's very sad however they had to go through such a traumatic experience to prove it," she said.
The Australian Navy intercepted a boat carrying asylum seekers near Ashmore Islands overnight.
The boat is carrying 51 passengers and four crew.
The people on board will be taken to Christmas Island for identity and health checks before they are assessed for refugee status.
- Australian Broadcasting Corporation
- © ABC