Australian Federal Police have been called in to investigate after Fairfax Media obtained and published the documents, which reveal concerns in government that the sweeping changes to the visa system could undermine social cohesion, increase the risk of violent extremism and create a "two-tier society".

Details of the proposed overhaul were examined by the powerful national security committee months ago and are now expected to go before the full cabinet in early 2017.

The reforms would involve the mandatory granting of a new provisional visa before a person can be granted permanent residency.

The changes are supposed to "reframe temporary, provisional and permanent migration and citizenship" and deliver budget savings by tightening access to social security payments for the newly created category of 'provisional migrant'.

In Parliament, Labor's legal affairs spokesman Mark Dreyfus asked if the leaking of sensitive and protected documents would be investigated by the federal police, "given the document refers to details of past and future meetings of the national security committee of cabinet"?

Prime Minister Malcolm Turnbull told Parliament the secretary of the Department of Social Services, Finn Pratt, had referred the leak to the AFP for investigation, while playing down the leak.

"The document concerned is not a cabinet document. It was not a cabinet document as such...it was marked protected because it was dealing with matters that were to be submitted to cabinet but was not, in fact, submitted to cabinet."

The document, which reveals details of national security committee and cabinet deliberations, was prepared for a meeting of Mr Pratt and his Immigration Department counterpart Michael Pezzullo earlier this month, and lays out a litany of concerns about the visa changes.

"The Minister for Immigration and Border Protection [Peter Dutton] is now seeking cabinet's agreement on the design principles for these eight new visas," the briefing document states.

"The proposed reforms could undermine Australia's social cohesion and potentially increase the risk factors that may lead to violent extremism by creating a two tier society where migrants are treated substantially differently to Australian citizens.

"Changing the longstanding national narrative to one which treats all migrants with suspicion does not best leverage migrants' willingness and potential to contribute."

In addition, the imposition of an additional waiting period for access to the social safety net for people holding a provisional visa would "likely contravene our international obligations, particularly for vulnerable migrants".

"Delayed access would have a particularly detrimental impact on the outcomes of the most vulnerable migrants, such as humanitarian entrants or those who experience domestic violence."

And it is not clear that "integration testing", the document notes, would "lead to improved understanding of and adherence to Australian values".

Finally, the briefing document warns that removing a direct pathway to permanent residence, and moving existing visa holders to the new system, would "likely be unpopular" in the community because one in two Australians were either born overseas or has a parent born overseas.

The Department of Social Services also said the visa proposal could have "significant flow on impacts" in other portfolios and that the "proposed timetable is too short" for consideration and implementation. It also warned the Immigration Department that the cost of the sweeping changes would be "huge" and the "savings may not be as significant as DIBP expect".

"This proposal has the potential to fundamentally change access to social security payments for newly arrived migrants, who already serve a waiting period before access to government services," the document notes.

It recommends people on a humanitarian visa be excluded from any social security access changes.

Labor's employment spokesman Brendan O'Connor seized on the leaking of the confidential document to highlight divisions in the Turnbull government.

"In relation to that matter, these are very sensitive issues, how we deal with permanent residents, temporary visas, people with citizenship, of course that should be dealt with very delicately and carefully. But the fact that that document is released means that there is fighting amongst cabinet ministers in this government and the fighting will not cease," he said.

The cabinet paper also states that humanitarian entrants – who would be placed on the new provisional visa under immigration's proposal – should continue to enjoy access to social security support as it "is key to their successful long term settlement".

The document also raises concerns about a separate, redeveloped Community Support Program that would reduce social security payments.

"If entrants are chosen on the basis of employable skills and English language proficiency...this approach undermines the rationale of the humanitarian program being based on need."

The leak has occurred amid growing debate about immigration in Australia. Mr Dutton recently introduced a bill to ban refugees and asylum seekers from Manus Island and Nauru who are resettled on a third country from ever being able to visit Australia, even on a tourist or business visa.

Comment has been sought from Mr Dutton and Social Services Minister Christian Porter.