Security agencies had no information to suggest the Australian man accused of the Christchurch mosque massacres should be placed on a watchlist or prevented from leaving the country.
Brenton Tarrant has now been charged with 50 counts of murder over the March 15 attack.
He also faces 39 attempted murder charges when he faces court again on Friday.
Home Affairs secretary Michael Pezzullo said Tarrant had spent just 45 days in Australia over the past few years.
Security and intelligence chiefs had no evidence to suggest the 28-year-old from Grafton in NSW posed a risk.
"There was no reason to restrict his movement because nothing had come to attention ... to suggest that he was on a pathway to violence," Mr Pezzullo told a budget estimates hearing in Canberra on Thursday.
"There was nothing in any of our systems that would have suggested that either this person's travel be restricted, or that he otherwise be the subject of law enforcement attention, up to and including arrest."
Tarrant travelled extensively since 2010 before settling in the New Zealand city of Dunedin.
He is accused of shooting dead 50 people and injuring dozens more after opening fire in two mosques during Friday prayers, live-streaming the killing spree on social media.
Sixteen people remain in hospital, including a critically-injured four-year-old girl.
Tarrant is due to appear in a New Zealand court by video link on Friday, but is not required to enter pleas to the charges.
The procedural hearing is expected to confirm whether Tarrant intends to represent himself at trial.
The prospect has raised concerns the self-labelled white supremacist could use the legal process to espouse extremist views.
Much of Friday's appearance is expected to happen behind closed doors.
