TONY JONES, PRESENTER: This is an exclusive report from Canberra.

A highly sensitive government document obtained by Lateline has revealed a draft proposal for sweeping reforms to Australia's visa framework.

Under the proposed changes, refugees would no longer be granted direct access to permanent residency in Australia.

The leaked document also includes a warning about the 12,000 Syrian refugees coming to Australia and argues in favour of increasing monitoring of new migrants.

Let's go straight to Canberra for more from our Lateline's political correspondent David Lipson.

David, set this up for us, will you? The leaked document here, it's marked "protected, sensitive, cabinet". Does its recommendations, or does it mean its recommendations have already been to cabinet?

DAVID LIPSON, POLITICAL CORRESPONDENT: Tony, good evening. The honest answer to that is I don't know if this document has been to cabinet. Across every page of the document are the words - or is the word "draft", so clearly it's a draft proposal. But still, the actual actions that are proposed within it are very significant for Australia's migration intake. There are only two references to a date within the document. One is a previous meeting of the National Security Committee on 24th November, so it's clearly happened after that that this document was drawn up. The other is a mention of the Immigration Minister Peter Dutton putting into place some of these actions some time in the first half of this year.

TONY JONES: OK. Well you've spoken to the minister's office earlier this evening. What have they said about the status of the document?

DAVID LIPSON: Well, nothing - nothing obvious or nothing clear about the status of the document, other than to point out that it is a draft document, that many draft documents are prepared for government and discussed within government and many of them are not adopted by government. Let's take a look at the story we've prepared. We'll talk more after that.

Early September last year, as the migrants pouring into Europe from the Syrian conflict became a flood, in Australia, public pressure mounted on the Prime Minister to help. Reluctant at first to bring in additional refugees, on 9th September, Tony Abbott decided to act.

TONY ABBOTT, THEN PRIME MINISTER (September): Australia will resettle an additional 12,000 refugees.

DAVID LIPSON: At the time, the show of compassion was met with widespread praise, but just over a month later, everything changed.

The discovery of a Syrian refugee's passport on or near the body of a dead suicide bomber in Paris only heightened fears that violent extremists were trying to infiltrate the West, hidden amongst hundreds of thousands of legitimate refugees.

Now, a draft document obtained by Lateline reveals the extent of the Australian Government's concerns and the lengths it's prepared to go to keep radicals out of Australia. Marked "sensitive" and "protected", the document is believed to be recommendations for the Immigration Minister to take to the highly secretive National Security Committee. It cites links between terrorist attacks on Australian soil and Australia's humanitarian intake, pointing to the Martin Place gunman, Man Haron Monis, Parramatta police shooter Farhad Jabar and the Melbourne knife attack by Abdul Haider. All were either refugees or dependents of recent humanitarian migrants.

The document then the outlines a plan by Peter Dutton for sweeping changes to the nature of the humanitarian resettlement program that has served Australia for decades. "In the first half of 2016," it reads, "the Minister for Immigration and Border Protection will bring forward proposals to reform the visa framework and remove direct access to permanent residents to better align visa and citizenship decision-making with national security and community protection outcomes."

That would see bona fide refugees accepted by Australia no longer given the certainty of a life here.

The document refers to, "... a package of reforms to simplify Australia's visa framework and create stronger controls over access to permanent residency and citizenship." They include: an enforceable integration framework to assess aspiring migrants' suitability for life in Australia, a revamped Citizenship Test and Citizenship Pledge and enhanced access, use and protection of sensitive information to strengthen intelligence-led, risk-based decision making... from pre-visa stage through to post-citizenship conferral.

Presumably, that would mean refugees brought to Australia under its humanitarian program would be closely monitored, even after they become Australian citizens.

There are also specific concerns raised about the 12,000 additional Syrian refugees.

"... it is expected that some refugees from this conflict will bring issues, beliefs or associations that lead them to advocate or engage in politically motivated or communal violence."

The expected surge of migrants from Syria has now slowed to a trickle. Priority is being given to families and children and those considered to be vulnerable. Just over 20 people have arrived here as the Government ramps up its security checks.

This week on Lateline, Minister Dutton again outlined some of the measures the Government is taking.

PETER DUTTON, IMMIGRATION MINISTER (Tuesday): We look through each of those cases to make sure that the bona fides are established, and as I say, very importantly, we conduct biometric tests and conduct those tests in a very rigorous way and we work with our US, UK and Canadian partners to make sure that we can mitigate any threat that might come from people that would pose themselves as refugees but aren't true refugees.

DAVID LIPSON: But the document also outlines another way refugees are being selected. It says, "Australia is prioritising family groups who have been registered with UNHCR for lengthy periods to further reduce the potential for deliberate extremist infiltration."

That would mean those fleeing some of the most deadly recent months of the conflict are unlikely to make it to Australian shores.

TONY JONES: So David, I'll just pick up on a couple of those more controversial recommendations spelt out here. The first item is under the heading "Mitigating risk to the community" and it says, "We're going to reform the visa framework and remove direct access to permanent residence." Is it clear what Mr Dutton means by that?

DAVID LIPSON: It's not entirely clear. We can only really guess what he means to that. I took that as actually meaning that the automatic permanent residency that is granted to bona fide refugees that are accepted by Australia will no longer stand; that is, that there would be some sort of uncertainty as to their future in Australia until they can be at some point declared safe.

TONY JONES: It's unclear what this means for people who already are permanent residents, who have that status. Nothing in the document about that?

DAVID LIPSON: Nothing in the document about that. My guess would be that they would be clear. This would be referring to any new migrants coming to Australia under its humanitarian program, but these are the sorts of questions that we'll have to put to the Immigration Minister.

TONY JONES: OK. Under the headline "Measures to mitigate radicalisation risk, an enforceable integration framework". What would that be? Any idea? Is there any flesh to those bones?

DAVID LIPSON: Look, the only two things that are mentioned is the revamping of the citizenship test and also the citizenship pledge. As to what that revamp would mean and see happen, it's not clear. The other thing is the sort of looking into migrants' suitability for life in Australia. So that's an element we haven't really heard before from the Government and how that would be assessed and carried out remains unclear as well.

TONY JONES: OK. One of the most controversial ones, long-term intelligence monitoring, so it appears, of refugees from pre-visa stage to post-citizenship conferral. That's a very long period of monitoring, potentially years.

DAVID LIPSON: Well exactly and this is the most interesting part of this whole document to me because it suggests that even after refugees have been living in Australia for some time, probably working in Australia, integrated within the community and become Australian citizens, even after that, then they may still be monitored by the Government, and that is obviously one set of rules for some citizens, a different set of rules for others.

TONY JONES: Now here's another part of the document which we haven't talked about in your story that is going to lead to significant community debate, one suspects. They've cited in the document the case of the intake of Lebanese Sunni Muslims during the Lebanese Civil War as an example of what not to do in the future.

DAVID LIPSON: Yeah, this is a really interesting element of this document. It points to some of the measures that were taken between 1975 and 1990 when there was that surge of Lebanese refugees from the Civil War there and the fact that it was very difficult to do background checks because the Lebanese Government wasn't really operating at the time, the fact that the Government here in Australia had to loosen some of the arrangements and definitions of refugees and also the fact that certain of those refugees came from sort of poorer rural communities, led to all sorts of problems within the Australian community that went on for some years, problems involving, you know, a lack of integration and also some issues relating to radicalisation or at least susceptibility to it.

TONY JONES: It is bound to be controversial, though, focusing in on one section of one ethnic group in Australia. And there's a Recommendation F here that says, "Recent overseas examples and Australia's historical experience with the Sunni Lebanese community illustrate potential community safety and national security risks associated with unsuccessful integration." That's going to cause community debate.

DAVID LIPSON: Yeah, it certainly will, particularly among members of the Lebanese community. It's interesting that the Government, you know, pointed to that as a sort of lesson to be learnt for the current wave of migrants or refugees coming to Australia and that'll upset some people, for sure.

TONY JONES: It leads us - all those problems you talked about, including them not actually being UNHCR refugees, led to this point 21: "Consequently, this led to the transportation to Australia of a Sunni community which included elements who already held extremist beliefs, or who were more highly receptive to extremist messages." I mean, these lines are going to be out there for debate now. One wonders why the Government would've focused so clearly on one group, a Muslim group, a Sunni Muslim group in particular.

DAVID LIPSON: Well, remember in terms of this document that this is, well, number one, a draft document, but it appears to be a document for the Immigration Minister Peter Dutton to actually take to NSC. It's not government policy at this point. As to whether it's Peter Dutton's view, we don't even know that either. But clearly, it was being considered at one point and you'd imagine has crossed his desk.

TONY JONES: OK, so finally, the document at the end does contain a kind of warning about the 12,000 Syrian refugees. What does it say?

DAVID LIPSON: Yeah, well, the warning about the Syrian refugees essentially is that even after all the integration efforts, all the support that the Government gives those refugees in terms of education, English lessons and the like, that there is still a potential risk of radicals actually getting through the net and making it to Australia. So this really just highlights the concerns that have clearly framed this entire document, that elements of the Government have with the fact that these 12,000 refugees are coming in from a real hot spot, a danger spot of the world.

TONY JONES: In fact, specifically, here's what it says: "Some will bring issues, beliefs or associations that lead them to advocate or engage in politically motivated or communal violence." Perhaps that's realistic, but I suppose once again, the community's going to be wondering: if they already know that's going to happen, why are they spelling it in out in documents like this? Why don't they do something about it? There is one other thing. At the end of the document it says they are going to have a longitudinal study of this 12,000 done by the department.

DAVID LIPSON: Yeah, yeah, that - excuse me - is exactly right and exactly what that longitudinal study will mean, we don't know. Again, questions for the Immigration Minister.

TONY JONES: Thank you very much. Obviously there'll be on this in coming days, but thanks so much for that, David.

And we did of course try to contact the minister for comment on that story. He was unavailable.