These people had not come “the right way”, Morrison told a news conference on Wednesday.
“I want to be very clear about that. I want to send a very clear message to people smugglers in the region that nothing’s changed.
“I will not give you a product to sell and take advantage of people’s misery. My government won’t do it. We never have and we never will.”
Government sources say there are more than 4500 Afghans in Australia on temporary protection visas, almost all of whom arrived by boat.
Although Morrison is adamant they will not get permanent residency, the government is making it clear there will be no attempt to return them to Afghanistan as things stand.
Opposition leader Anthony Albanese is among those who have called for them to be granted permanent residence.
The government announced on Wednesday an initial 3,000 humanitarian places would be allocated to Afghan nationals within Australia’s 13,750 annual program which runs over a financial year.
Immigration Minister Alex Hawke said the government would give Afghan nationals “first priority” within the offshore humanitarian program. The priorities would be family members of Australians, and those facing persecution including women and girls, the Hazara, and other vulnerable groups.
Some 8,500 Afghans have been resettled in Australia since 2013 under the humanitarian program.
Hawke said the government anticipated the initial allocation would increase further over the course of the year.
Morrison stressed: “We will only be resettling people through our official humanitarian program going through official channels.
“We will not be allowing people to enter Australia illegally, even at this time.
“Our policy has not changed. We will be supporting Afghans who have legitimate claims through our official and legitimate processes. We will not be providing that pathway to those who would seek to come any other way. That is a very important message. The government’s policy has not changed, will not change.”
As the government scrambles to evacuate people who assisted Australian forces in Afghanistan, Australia’s first evacuation flight from Kabul took only 26 people. Morrison said they included Australian citizens, Afghan nationals with visas, and one foreign official who had been working with an international agency.
The Afghans being brought to Australia in the evacuation are not included in the 3000.
Morrison emphasised the difficulty of assessing those Afghans seeking to come to Australia on the grounds of having helped Australian forces.
“They may have worked for us four years ago or five years ago. And we knew where they were then.
“And we may not have heard from them for a very long time. And we don’t know what they’ve been doing in that intervening period in what has been a very unstable situation.
“So it isn’t just a matter of people coming along and presenting, you know, a payslip from the Australian government saying, ‘I used to work for you’. I wish it were that simple.”
The Refugee Council of Australia said in a statement: “Permanent protection is needed for the 4300 Afghans on temporary protection visas, recognising that members of this group are unlikely to be able to return in safety for many years to come and need the assurance that they can continue to live in Australia without the constant fear of forced return.”