The creation of the Home Affairs mega-portfolio has cost taxpayers $5.5 million, coming in at just over half its predicted budget.
Most of the money has gone towards creating secure office space and IT infrastructure to handle "top secret" traffic, a Senate committee has heard.
Australia's immigration, border, law enforcement and domestic security agencies were merged in December into a single department overseen by minister Peter Dutton.
The federal government had budgeted $10 million to establish the department.
It is home to about 14,000 staff and the overall portfolio is overseen by Mr Dutton who has about 24,000 staff.
This year's federal budget outlined plans for Home Affairs to achieve $256 million in savings through "efficiency measures" over the next five years.
Department secretary Michael Pezzullo is confident the cuts won't affect frontline capabilities.
"You should be able to make advances in areas such as property, shared services, IT and the like," Mr Pezzullo told the Senate estimates hearing in Canberra on Monday.
"Now it's the hard-grinding work, as is always the case with anticipated savings, to work out the specifics of how we're going to achieve each and every item of that broad plan."
Mr Pezzullo said changes across portfolio agencies since the merger had already improved the country's response to terrorism, cyber and transnational crime, foreign interference and threats to critical infrastructure.
"We now have the framework in place to tackle these questions with clear lines of authority, singular purpose and pooled capabilities in place, none of which were evident before the establishment of the portfolio," he said.
"Previously, these functions were broken up and dispersed across a number of departments and agencies which did not necessarily have a primary focus on domestic security and law enforcement."
He pointed to the country's counter-terrorism tsar working on strategies to ensure those who travel to the Middle East to fight with terrorist groups are dealt with "as far from our shores as possible".
The department is also examining ways to strip dual nationals "who no longer maintain an allegiance to Australia" of their citizenship.
Mr Pezzullo talked up the slated establishment of an Australian Centre to Counter Child Exploitation to fight the abuse, torture and murder of children.
"The centre will hunt online and will be able increasingly to use all of the weapons at our disposal to deal lawfully with the most evil acts perpetuated on this earth," he said.
Australian Associated Press
