Prominent in the saga are Prime Minister Scott Morrison's claims that he "stopped the boats" and secured Australia's borders from asylum seekers. For some years, these claims have been systematically debunked by a former Immigration Department head, John Menadue, and two of its former deputies, Abul Rizvi and Peter Hughes, on Menadue's website, Pearls and Irritations. So-called "mainstream media" have neglected this debunking, to the point where journalist Peter Hartcher told readers recently: "Scott Morrison was the immigration minister who restored control of Australia's borders."

So what is the truth? In September 2011, Morrison, Tony Abbott (who was then opposition leader) and the Greens blocked legislation that would have permitted the so-called "Malaysian solution", which, in all likelihood, would have significantly deterred asylum seekers. Without the legislation, 591 boats brought in 39,070 people to Australia from October 2011 to July 2013. Abbott has since expressed some regret about his role in this; Morrison has not.

In July 2013, the then prime minister, Kevin Rudd, announced that no one arriving by boat would be settled in Australia. His government also accelerated the assessment of Sri Lankan asylum seekers, quickly returning many home, while Indonesia slowed the arrival of people to its shores by introducing visa requirements. Immediately, the number of boat arrivals fell dramatically. When the Coalition won office towards the end of September, 829 people arrived by boat that month compared to 4230 in July. In December, Morrison, after he became immigration minister, began turning boats back.

In knocking off the Malaysian solution, Morrison may have effectively allowed about 30,000 asylum seekers to arrive by boat. As Menadue has written, Morrison (and Abbott) didn't want to stop the boats; they wanted to stop Labor from stopping the boats. When be became a minister, Morrison adopted Rudd's policies, added boat turn-backs and the supply of asylum seekers continued to decline – as it almost certainly would have without him. In large part, Morrison's operation sovereign borders was a publicity stunt.

Nevertheless, asylum seekers are arriving in greater numbers and at an increasing rate by the safer and cheaper means of aeroplanes. In the year ending June 2018, 27,931 people with visitor visas, the bona fides of which may be difficult to assess at points of departure to Australia, applied for protection visas, compared with 18,365 boat arrivals who made like claims in 2012-13. The backlog of applications for protection visas at June 2018 was 177,140. The backlog of appeals on all migration and protection/refugee visa applications to the Administrative Appeals Tribunal increased from 17,480 in 2016 to 52,491 in 2018.

In other words, Morrison and Peter Dutton have allowed the arrival of asylum seekers to spin out of control. By not clearing visa applications quickly, so allowing people to remain in Australia for long periods, they have provided extra incentives for people to try their luck on visitor visas. More asylum seekers are arriving by plane than did by boat, while delays in finalising their cases have provided an immense amount of work for those helping them get the visas they desire. As they wait in the queue, many seem to fall into the hands of unscrupulous Australian employers who sweat the devil out of them. It's a considerable achievement and one diametrically at odds with the government's excited rhetoric.

And it's not as if that rhetoric is only being used to hide the truth. It is being used as a political lever to encourage fears about outsiders, making the effective settlement of the current high number of migrants more fraught.

Dutton, the Home Affairs Minister, uses alleged crimes by a few to tarnish whole groups. Morrison and Finance Minister Mathias Cormann rattle on about rapists and murderers in detention centres as if most people in those hellholes are guilty of such crimes. Department of Home Affairs secretary Mike Pezzullo obsesses about a grossed-up threat of terrorists lurking around every corner in his imaginings of a "dark universe" of "global contract hitmen" and "fly-in assassins". (Could he tells us how many fly-in assassins have plied their trade in Australia in the past five years?) Most recently, when Morrison failed to get his way with laws on the medical evacuation of detainees in Nauru and Manus Island, the Prime Minister unconvincingly alleged this would attract the boats again, indulged in hyperbole that just might encourage some to give it a go and then said that, if they did, he'd blame his political opponents.

The thinking, if that's not rating it too highly, behind this language has institutional consequences. These consequences are not confined to delays in visa processing but extend to making it gratuitously more difficult to obtain citizenship through longer waiting times, harder tests and more stringent qualifications. The debauched language of the immigration debate is also reflected in the administrative structure of the federal government, most notably the home affairs portfolio, now not long just past its first birthday.

The creation of this portfolio offends just about all generally accepted principles of machinery of government. Departments should be built around services to be performed rather than groups or individuals to be served. Like functions should be co-located. Police, prosecutorial and intelligence-gathering should be kept apart from related policy functions. And major responsibilities, like immigration, should have standalone departments.

Ministers and Pezzullo's justifications for the home affairs portfolio are not couched in these terms; they're hollow and lack intellectual respectability. Pezzullo says "we are all one function ... wielding state power to keep our fellow citizens safe and secure". Such hogwash exposes the distinguishing feature of home affairs: a stink of empire building at both the political and bureaucratic levels.

The home affairs portfolio includes immigration, customs and multicultural affairs, and a range of security-related functions, including what its website refers to weirdly as "countering terrorism policy". Organisationally, the department has an astonishing 10 deputy secretaries, some responsible for only one division. Deputy secretaries are supposed to relieve department heads from difficult spans of supervisory control; home affairs has used them to create that very problem.

Border Force contains customs and other functions. Its staff are uniformed and some are armed. It is supposed to be "operationally independent" but its budget and employing authorities are held by department secretary. The Australian Federal Police, the Australian Criminal Intelligence Commission, AUSTRAC and ASIO are also in the portfolio.

In its short life, the portfolio has racked up an impressive number of administrative bungles, not just on Fijian citizenship and Interpol red notices but on major matters exposed by the Auditor-General. The more serious strike against it, however, is that it has allowed a range of unrelated functions to smother and corrupt immigration policy development and administration.

Immigration is about people; customs and excise administration is about goods. While immigration authorities need to exercise a quasi-policing role and be able to detain people who arrive in the country without their claims and fitness having been assessed, the government's immigration function is fundamentally about bringing in people the country wants and needs, and helping them adapt quickly. Immigration is not essentially about "keeping our fellow citizens safe and secure"; it's about nation-building in many guises, including supporting the labour market, economic growth and prosperity.

Notwithstanding its infancy, it's time to call the creation of the home affairs portfolio for what it is: a failure that should be unpicked before it gets worse, regardless of who wins the forthcoming election.

The first step should be to create a department of immigration and citizenship headed by a senior cabinet minister. It would contain all immigration functions, including visa compliance, together with migrant settlement, language education and other migrant-support programs that were dispersed to other departments.

Second, a customs and border agency should be created to house most of the existing Border Force's functions, perhaps with staff clothed in uniforms of a more pastel shading. The agency would be well placed in the attorney-general's portfolio.

Third, as political policy imperatives can skew police and intelligence-gathering, the federal police, crime commission, ASIO and AUSTRAC should be placed back in the attorney-general's portfolio. Facts should inform policy, not be made to fit around it.

Fourth, remnant home affairs functions should be distributed to other ministers and their departments and agencies in accordance with generally accepted principles of machinery of government.

It's unlikely the present government, either now or if it is re-elected, would have the slightest interest in such changes. It seems to want to keep using immigration for political advantage as much as it can. Morrison's recent disclosure of advice from officials about the reopening of detention facilities on Christmas Island following the medivac legislation is just the latest example of such impulses, which politicise and discredit agencies.

Labor, however, should reflect closely on the damage being done to immigration by having it in the home affairs portfolio. It should also think closely about the political dangers of maintaining an accident-prone organisation based on little more than empire-building by members of the old regime. There are, of course, risks and costs associated with a major reshuffle and the distribution of home affairs functions, though they are unlikely to be as great as the risks and costs of maintaining the present structure.

Fixing the machinery of government will not of itself restore sanity, decency and honesty to immigration policy and administration. Indeed, the parlous condition of that machinery is in many ways a symptom of the appalling way in which immigration is often discussed. The most important thing is to lift the standards and quality of debate so it becomes an effective influence on policy, rather than be used as a political meat grinder.

There would be value in establishing a royal commission on population policy and Australia's immigration future, with powers to require the production of documents and take evidence under oath. It should take into account regional geopolitical and population trends, including Australia's labour-market needs, and environmental considerations. It should recommend longer-term population policy and how immigration could support that policy, consistent with broad economic goals.

At times, immigration has been lucky enough to be based on genuine bipartisanship rather than the current rough consensus forced by political opportunism. Immigration needs to be refreshed and renewed around a new consensus based on the public interest. A royal commission could help do that in ways that seem, at the moment, to be beyond the will or ability of politicians left to their own devices.

Paddy Gourley is a former senior public servant. A version of this article first appeared in Inside Story. Email: pdg@home.netspeed.com.au