Home Affairs transition cost $2 million

The creation of the Home Affairs mega-portfolio has cost taxpayers roughly $2 million so far.

Australia's immigration, border, law enforcement and domestic security agencies were merged in December into a single department overseen by minister Peter Dutton.

"If (transition costs) came in over $10 million I'd be asking some pretty hard questions," Home Affairs Secretary Michael Pezzullo told a budget estimates hearing in Canberra on Monday.

Some works are still under way to boost security measures at Home Affairs offices, but Mr Pezzullo is confident the costs won't spiral out of control.

"You'll need a very powerful telescope to see the transitional costs against the scope of resources coming in," he said.

The Home Affairs Department has about 14,000 staff and the overall portfolio overseen by Mr Dutton has about 23,000 staff.

Mr Pezzullo lashed out at criticisms of the new mega-department as "flights of conspiratorial fantasy", rebuking suggestions there was some sort of sinister concentration of power at play.

In his former role heading the department of immigration and border protection, Mr Pezzullo took home an annual salary of $745,000.

The secretary took on notice questions about his new pay packet and confirmed his salary had increased to $788,000 a year.