The Immigration Minister Peter Dutton is defending his introduction of the October 1 deadline despite the threat of possible legal action from refugee advocacy groups.
Mr Dutton said over the weekend that asylum seekers he has described as "fake refugees" would be deported if they do not submit an application for a protection visa by the deadline.
The measure is relevant to about 7,500 asylum seekers.
Following the backlash from refugee advocates, he has told the Nine Network he is not interested in hearing it.
"I mean, these are people who've been here for maybe five, six or seven years, claiming to be refugees, but won't provide any information, won't answer the questions, in some cases, won't even provide information about their identity. And they expect me to grant visas, allow some people to become citizens, when we don't even know the identity of these people. So, look, the lawyers can rant all they want, from my perspective."
The principal solicitor for the Refugee Advice Casework Service says Government claims that some asylum seekers have had five years to lodge applications are true.
But Sarah Dale says, also, the delay has been due to government restrictions.
"So, absolutely, there are people who have been in Australia for five years. What is really misunderstood is that people haven't had an opportunity to apply for their visas on arrival in Australia. We had a policy where people that arrived by boat were only able to apply for visas once invited by the Department of Immigration to do so. There are people who have only received those invitations at the end of last year. So the statement that all these people have had five years to lodge their claims for protection is utterly false."
The crossfire over the new application deadline comes as details also emerge about a shooting at the Manus Island detention centre that run counter to the Government's version.
Australian officials have now confirmed nine people were injured during the April 14 shooting after earlier saying no one was hurt.
Department of Immigration head Michael Pezzullo has told a Senate committee hearing it has since become clear many more shots were fired.
And, contrary to Mr Dutton's original account of only shots fired into the air, Mr Pezzullo says a number of shots were "fired laterally" into the centre compound.
He says the incident is the subject of two separate investigations.
"In the circumstances, given the seriousness of the matter, the best course of action -- and one that I thoroughly endorse -- is to then await the conclusion of the two relevant inquiries. One is the military justice inquiry. The other one is the criminal justice inquiry in the civil jurisdiction. And then, if we have more to say at that point, we will say more at that point."
Mr Dutton has repeatedly said Papua New Guinea soldiers opened fire on the centre after local anger over a young boy allegedly being led into the compound by detainees.
Amnesty International has investigated the shooting and disagreed, also finding shots were fired into the centre.
Refugee coordinator Graham Thom says it is just the latest incident on Manus and is calling on the Government to take action to protect detainees.
"We need to make sure that the Department of Immigration actually articulates what is going to happen to these men who are about to be put out into a community on Manus Island where it is undoubtedly unsafe for them, where they will experience violence. We have seen this before. We know this is going to happen again. And, yet, we have no clear idea of how their safety will be protected."
The Government has announced the centre will shut down on October 31.
It has said asylum seekers will be given the option of settling in Papua New Guinea, transferring to countries other than Australia or returning to their countries of origin.
