The Immigration department has not been militarised, according to its boss Michael Pezzullo.
The departmental secretary, who was revealed this week to have the confidence of only 30 per cent of his staff, says that change is unsettling and that some decisions will not please everybody in the department.
In a joint statement with Border Force Commissioner Roman Quaedvlieg, Mr Pezzullo said the dismal results of a staff Pulse survey, revealed this week by Fairfax Media, reflected "legitimate concerns" of his staff but the benefits of the merger with Customs were already being seen.
Staff complained in the survey of a "command and control" approach, a "military-style regime" and a culture of blame for failure that came from the top.
But Mr Pezzullo and Mr Quaedvlieg are unhappy with being accused, again, of militarising the department.
"We reject categorically the inaccurate and unhelpful meme that the department has a 'militarised' culture: the only staff required to be in uniform and to carry weapons are those whose duties require it and who are properly credentialed and trained," they wrote.
The two men also say the transition to a "fresh" culture will not occur overnight.
"Already we are seeing benefits in establishing blended teams of former Immigration and Customs who are working with new colleagues who bring specialist skills in areas such as intelligence, analytics, investigations and operations," they wrote.
"Effecting this workforce transition, and with it a fresh culture, will take time."
"Change is unsettling; it leads to uncertainty, so it is not unusual or unexpected to see survey results that bear out the legitimate concerns of our staff. Some decisions won't please everyone but that is not an excuse to resile from them.
"We need to work with our people to equip the organisation to meet the demands of the future."