To complete setting up the new mega security Department of Home Affairs, the federal government is amending a lot of legislation. But not all of the changes are being presented willingly for public scrutiny.

This week, the government produced the raft of amendments parliament must pass to finalise the amalgamation of Immigration and Border Protection with security and intelligence agencies including the Australian Federal Police, the Australian Criminal Intelligence Commission, the Australian Transactions Reports and Analysis Centre, known as AUSTRAC, and the Australian Security Intelligence Organisation, or ASIO.

There are 284 changes, amending 33 separate acts, to complete the transfer of ministerial authority over these agencies from the attorney-general to the minister for Home Affairs, while preserving the attorney-general’s role in approving ASIO investigation warrants and special operations.

But 47 of them relating to ASIO were being kept from public view.

The high-powered parliamentary watchdog on security matters, the parliamentary joint committee on intelligence and security (PJCIS), recently reviewed the first part of the Home Affairs and Integrity Agencies Legislation Amendment Bill and published its report, recommending some changes.

On March 1, the committee received the rest of the amendments and this week, following usual practice, published the list of them on its website to indicate the start of this next review.

The amendments were all numbered according to the alphabetic order of the acts they affected. Without explanation – and in a significant departure from usual practice – three sets of the numbered amendments were missing.

They relate to the ASIO Act and the Telecommunications (Interception and Access) Act and are the most controversial of the amendments being proposed – a point the committee effectively acknowledged when it recommended in its earlier report that parliament not vote on the Home Affairs bill until the amendments to these acts had been introduced and, by inference, scrutinised.

When Minister for Home Affairs Peter Dutton takes over management of these guidelines, his department will be responsible for any future reviews and the redrafting of them – effectively a direct role in the oversight of ASIO.

The government-dominated committee is one of the most important in the parliament and is made up of MPs and senators from the two major parties.

It forms a key part of the oversight of Australia’s intelligence community and plays a significant role in scrutinising governments’ legislative plans on security.

It examines ASIO-related amendments, even the most basic, as a matter of course.

Some of its work is conducted in secret and its members face criminal penalties for disclosure.

But much of it is necessarily public, part of the oversight that exists to reassure Australians someone is checking what governments and their security agencies are doing.

Right now, it has a huge workload because of a bundle of security-related bills the government wants passed – including the one creating Home Affairs.

Prime Minister Malcolm Turnbull rushed a package of four pieces of legislation – the Home Affairs bill, plus others covering espionage and foreign interference and foreign influence – into parliament on the evening of December 7, immediately after the House of Representatives voted on same-sex marriage and while advocates of the change were still celebrating in the chamber and the galleries above.

Turnbull declared all amendments essential for national security.

In evidence to the joint committee inquiry into the foreign influence, interference and espionage bills, the acting Inspector General of Intelligence and Security revealed that the IGIS had not been consulted in advance of any of the legislation – changes to the law that affected his role.

Asked when the IGIS office first saw the legislation, acting IGIS Jake Blight said: “On 7 December, 2017. That’s the day it was tabled in parliament. That’s the day we saw it.”

Amendments to several of the bills are now being sent back to the government for redrafting because they don’t do what they are designed to do or in some cases appear to do the opposite.

Those in the security community frustrated by the haste with which all of this is being done repeatedly mention one word: “sloppy”.

The ASIO-related amendments are sensitive because there is some concern within ASIO and sections of the wider security community that shifting ASIO to the Home Affairs portfolio might diminish its independence and leave it vulnerable to political interference.

The new department’s secretary, Michael Pezzullo, has said the concerns are unfounded and condemned what he says is scaremongering about his powers.

But the retiring attorney-general, George Brandis, echoed those concerns in a private farewell speech he gave to ASIO last month, in which he also queried Pezzullo’s ambitions.

Of the agencies being transferred from the Attorney-General’s Department to Home Affairs, ASIO is the only one that has not yet moved. Its shift is contingent on the passage of the legislation.

Those are the amendments now before the committee – and, only as a result of inquiries by The Saturday Paper, before the public, too.

Following questions from the paper, the amendments were added to the list late on Thursday.

Attorney-General Christian Porter had originally provided the redacted version of the amendments, arguing that the committee’s own previous report suggested it did not need to examine them.

They are mostly administrative, but two in the ASIO Act relate to the power to make or remake guidelines governing ASIO’s activities. That power will now rest with Home Affairs Minister Peter Dutton – but he will have to consult Attorney-General Christian Porter first.

Asked why the amendments were not included in the first place, Porter told The Saturday Paper: “Nothing about these amendments is secret. Labor has had all of the amendments since 28 February and subsequently agreed on 2 March that only those administrative amendments not relating to the committee report would be referred for consideration by the PJCIS. This agreement excluded the amendments to the ASIO Act and TIA Act.”

Porter said they were excluded because of a recommendation in the previous report that said the amendments should be put to parliament for examination before the whole Home Affairs bill was voted on.

Shadow attorney-general and member of the committee Mark Dreyfus dismissed Porter’s explanation.

“It seems the new attorney-general doesn’t understand the important bipartisan role that the intelligence committee fulfils. Mr Porter’s attempt to prevent that committee from considering a raft of changes to two of our most critical national security acts, including his own colleagues, as well as hiding those changes from public scrutiny, does not augur well for the approach he brings to his role.

“The committee recommended that the government bring forward amendments to the ASIO and TIA Acts. Mr Porter’s claim that the committee therefore has no further role in reviewing the extensive amendments now that they have been drafted is plainly nonsense.”

In the 40 years of ASIO’s existence, legislation related to its operations has always been made public to enable scrutiny before it is passed.

When Minister for Home Affairs Peter Dutton takes over management of these guidelines, his department will be responsible for any future reviews and the redrafting of them – effectively a direct role in the oversight of ASIO.

This is despite the new Home Affairs Department secretary telling a Senate committee recently that his department “will not engage in the oversight of statutorily independent agencies”.

ASIO’s most recent annual report revealed the Attorney-General’s Department was reviewing the guidelines, which are publicly available, at the committee’s recommendation. These guidelines currently limit ASIO’s reach and effectively entrench the right to peaceful protest and other lawful political activity in Australia.

With responsibility for the guidelines now to be transferred to Home Affairs, the status of the attorney-general’s review is unclear.

The amendments that had already been available for public scrutiny also raised some questions.

Some provide for shared authority between the attorney-general and the Home Affairs minister – for example, in authorising the laying of undersea communications cables through protected areas – and it is not clear who is actually in charge.

It’s also not clear if this is deliberate or a drafting error.

The government has already agreed to redraft other elements of important security legislation – relating to foreign influence and espionage – because of concerns raised in evidence to the joint committee about their impact.

The new amendments to a bill covering espionage and foreign interference will narrow the previously proposed definition of what causes harm to Australia and the scope of offences involving private citizens as opposed to Commonwealth officials. They also strengthen the original defences available to professional journalists receiving information.

The initial omission of the sensitive ASIO and telecommunications intercepts amendments from the public list of changes is not the only unorthodox move the joint committee has made in relation to ASIO this week.

It was due to complete its review of ASIO’s questioning and detention powers by Wednesday.

These powers allow ASIO to question people – and in some cases detain them – if it believes they have information relating to a terrorist act, past or future, even if they have no personal involvement.

Although the joint committee says it has completed the review – which usually also means the report is ready for publication – it has not yet presented its findings.

Committees routinely seek extensions of time for reporting on complex inquiries. The joint committee is in a special category because of its legislated status and role in overseeing intelligence agencies and this inquiry is itself specially entrenched in legislation, with its deadline laid out in the Intelligence Services Act.

Two minutes before the House of Representatives began its adjournment debate on March 1, ahead of rising for three weeks, the committee’s chairman, West Australian Liberal MP Andrew Hastie, tabled two other reviews of counterterrorism legislation and then mentioned the ASIO powers review that was due six days later.

“The committee has completed its review and is currently in the process of finalising the report,” Hastie said. “I expect to be able to present the committee’s report to the House in the near future.”

Generally, committee deadlines are not just for completing the review, they are for reporting to the parliament. If extensions of time are required, they are usually obtained before the deadline.

The joint committee is likely to seek an extension to resolve what are believed to be contradictions in some of the evidence, including from ASIO, about whether the questioning-and-detention powers are still required.

There is a growing list of significant figures involved in overseeing the intelligence agencies arguing that while ASIO’s questioning powers should stay, the powers combined with detention are excessive.

ASIO’s questioning-and-detention powers were legislated after the September 11 terrorist attacks in the United States and the Bali bombings in 2002.

But in recognition of their potentially serious implications for human rights, there has always been a sunset clause.

Under the current clause, they are due to expire in September this year unless extended.

Under division 3 of part III of the ASIO Act, the agency can obtain a warrant from an “issuing authority” for a person to appear before a “prescribed authority” for questioning to obtain intelligence about a terrorism offence, past or future.

If the agency believes that person may not appear, may destroy or damage evidence, or may alert someone involved in a terrorism offence, it can also apply for a detention warrant.

The person does not have to be suspected of involvement in the offence to be questioned and detained under these powers, simply to be reasonably suspected of having important information.

He or she can then be detained and held incommunicado – without contacting a lawyer before being questioned – for seven days. They can be questioned for up to 48 hours within that time.

Refusing to appear before the “prescribed authority”, refusing to answer questions or hand over relevant items, and giving false information, are all punishable by five years’ jail.

None of Australia’s so-called Five Eyes security partners – the United States, Britain, Canada and New Zealand – have such extensive powers.

In its submission to the committee, ASIO argues for its questioning powers to be extended, saying the threat environment has changed and the powers need to change, too.

This is despite a series of reports – from three consecutive Independent National Security Legislation Monitors, including the current one, and from the Inspector General of Intelligence and Security – saying the questioning-and-detention power is excessive and should be abolished.

The current IGIS argued that the existing questioning powers available to the Australian Criminal Intelligence Commission are an adequate model for similar powers for ASIO, both agencies being intelligence-gathering and not law-enforcement bodies.

ASIO has executed just 16 questioning warrants since 2003 and none since 2010.

The separate question-and-detain power that has also existed since 2003 has never been used.

It is not clear what the joint committee will decide to recommend, or when it will report.

It remains another puzzling and opaque dimension to the handling of national security, which no longer just leaves the spies in the shadows, but the legislative process as well.