Michael Pezzullo told a Senate estimate hearing on Monday the mega-department, announced in July, would be limited by checks on power and labelled claims to the contrary "fallacious and unworthy".

"Power must always be exercised with legitimacy and never more so than in the performance of the security function of the state," he said.

"Any contrary suggestion that the establishment of Home Affairs will somehow create an unchecked extrajudicial apparatus of power is ill-informed, even if predictable coming from some quarters.

"It is commentary which bears no relationship to the facts or to how our system of government works."

Mr Pezzullo, the architect of the Home Affairs department taking in Immigration, ASIO, the Australian Federal Police, Austrac and the Australian Criminal Intelligence Commission, has been subject to accusations of "empire building".

The proposal was hotly contested within the uppermost ranks of the government, and both minsters and officials complained it was unnecessary and potentially counterproductive.

Supporters of the merger have argued that it would improve co-ordination across the government in preventing terrorist attacks.

Mr Pezzullo said any executive actions within Home Affairs must have prior legal authority, to be given by parliament.

"In bringing together the security powers, capabilities and capacities of the Commonwealth into a single portfolio, these fundamentals will of course remain in place," he said.

"That is constitutionalism, the sovereignty of parliament, and the supreme rule of law. All of which are crucial attributes of liberty."

Mr Pezzullo revealed that, subject to Prime Minister Malcolm Turnbull's decision, the new department would be formed before February.

Australian Border Force would remain an operationally independent body, but would be connected to and have its corporate and enabling services provided by Home Affairs.

However commentary that the department would complicate agencies' work with another layer of administration was unfounded, Mr Pezzullo said.

"I can assure this committee that the department will not act as an overseeing, overriding bureaucratic layer, and nor will it be dictating terms to heads of agencies in the performance of their statutory functions," he said.

Home Affairs' role would be to improve the "strategic level of policy development and planning", and to support the minister-designate, Peter Dutton.

It would coordinate policy strategy and planning for domestic security, law enforcement, counter-terrorism, protection of sovereignty, and resilience of national infrastructure and systems.

Outlining the breadth of the department's scope of work, Mr Pezzullo said it would also deliver policy, either leading or supporting other agencies, for immigration and citizenship, transport security, biometrics and identity, cyber security, and customs and border protection.

Emergency management, including disaster recovery and resilience, and defending against foreign interference and political subversion would also fall within the department's remit.

Home Affairs' work would include countering violent extremism "including working with other departments regarding programs concerned with the cohesion of our society on the basis that it's open, inclusive, multicultural and united," Mr Pezzullo said.

Mr Pezzullo told senators the government would reshape the Attorney-General's department, which would adopt new roles from the Department of Prime Minister and Cabinet including oversight for intelligence and security.