When Malcolm Turnbull unveiled the biggest shake-up to the nation's security establishment in years, Australia's key anti-corruption body was mentioned just once, in passing.

This was despite the government's emphasis on accountability and integrity when announcing Peter Dutton's Department of Home Affairs. Unsurprisingly, the Australian Commission for Law Enforcement Integrity has featured in none of the ensuing public discussion, a fact that appears to be in keeping with tradition.

Peter Dutton will head the new Home Affairs ministry. AAP

In his almost four years as Justice Minister, Michael Keenan has not once requested that the commission hold public hearings to examine corruption – a move guaranteeing the agency's virtually non-existent public profile.

Fairfax Media is aware of several major investigations under way into the integrity of people or operations within agencies set to form part of Mr Dutton's new super-ministry. These investigations are being conducted behind closed doors by the integrity commission and the federal police.

Police will investigate corruption in Customs and Border Force, all under new ministry. Jessica Shapiro

The creation of Home Affairs means that the Australian Federal Police will now come under the same departmental umbrella as the people and agencies they are investigating in partnership with the integrity commission.

Experts warn the arrangement risks putting such integrity probes even further out of the public eye.

"Institutionally it is a weakness. The arrangements should be such that this is not an option," says Australian National University security expert John Blaxland.

Professor Blaxland has been critical of the proposed Home Affairs ministry because it may reduce the "high degree of healthy contestability" between agencies, which sees the AFP eager to scrutinise Border Force, and vice versa, when necessary. This is disputed by senior officials.

Professor John Blaxland is critical of the proposed Home Affairs ministry. Dion Georgopoulos

What is incontestable is that since its inception in 2006, the integrity commission has not held a single public hearing into any of the agencies it oversees: the AFP, the Criminal Intelligence Commission, Border Force and the Immigration Department.

Due to a lack of resources, Australia's least-known corruption fighting body relies on one of the agencies it oversees, the AFP, to actually carry out its major investigations.

Several of these joint investigations are under way. They include a probe into a Melbourne-based government agency insider suspected of helping an international criminal syndicate bypass border controls.

A second ongoing inquiry is targeting a network of Sydney contraband traffickers who have had highly irregular dealings with government officials. An associated case involves a government official who authorities suspect tipped off a notorious Sydney drug importer about a police operation.

Other major inquiries have been shelved for lack of evidence. These include a case in 2014 involving a now-former official from a government agency and a money launderer connected to a senior Asian politician.

In its most recent corporate plan, the integrity commission, known by its acronym ACLEI, says the corruption risks it confronts have "high potential impacts on individuals, Australian society and the economy – including by: aiding the illicit drug, counterfeit and contraband trades [and]… facilitating money laundering and terrorism financing".

The impact on the joint investigations of the reforms unveiled by Turnbull is unclear. One senior official says the shake-up is "logical" and likely to enhance the integrity commission's focus as it shifts from Justice Minister Michael Keenan's portfolio to that of the Attorney-General, George Brandis. But several officials in Canberra say there appears to have been limited thought, if any, about what the reforms will mean for the fight against corruption.

Professor Blaxland proposes an alternative: "I find the idea of a national ICAC [independent commission against corruption] attractive. There is a compelling case for it."

Senior staff inside Border Force also believe the current oversight model is failing. The agency referred serious allegations to the integrity commission two years ago. Since then, it has been left in limbo, unable to conduct its own internal inquiries and remove suspected staff.

"We want to get rid of them or do our own investigations, but we can't," says one senior official.

Despite intensive investigation work over many months, the two most serious corruption cases being investigated by the integrity commission and the federal police have yielded no public hearings and no criminal charges.

A report released on Saturday by the Australia Institute claims corruption commissions which hold public hearings are far more successful at exposing and prosecuting corruption. The biggest user of public hearings is the NSW ICAC. Since 2012, it has held 123 public hearings and referred 76 people to the state Director of Public Prosecutions, far more than any other state commission.

The institute's figures are open to interpretation. Queensland's corruption commission (which held its first public hearing this year) has referred 32 people for prosecution without the use of a single public hearing.

Former NSW director of public prosecutions Nicholas Cowdery argues the lack of accountability in the existing model is grounds for a national ICAC. So too is the fact that no agency has dedicated responsibility for investigating those outside of ACLEI's jurisdiction, including federal politicians. ACLEI also has no oversight over the Australian Tax Office, defence or other public sector agencies.

Mr Cowdery says concerns about the unfair smearing of reputations via public hearings can be managed by a commissioner who exercises his discretion carefully.

"Any half-competent commissioner can do it. Public hearings are vital because they give the public confidence that this work is being done," he says.

Senior officials who back the existing system of secret federal police and integrity commission investigations say it safeguards the reputations of those suspected of corruption but later cleared.

The Coalition opposes an ICAC, with politicians wary of the risk of a corruption commission chasing political scalps.

Veteran corruption fighter Tony Fitzgerald, QC, who is working with the left-leaning Australia Institute as it campaigns for a national ICAC, says those opposed to public hearings "demonstrate a fundamental ignorance of democracy".

"In a truly open society, citizens are entitled to full knowledge of government affairs. Information about official conduct does not become any less important because it diminishes official reputations," says Mr Fitzgerald.

Under the Turnbull security reforms, it is likely the attorney-general will retain the power to direct ACLEI to hold public hearings in the interests of exposing corruption.

Until that happens, or until the existing integrity commission lays charges or decides on its own accord to use its public hearing powers, some of the most serious corruption cases in Australia will remain hidden.

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