The Canberra Times reported on Tuesday that some workers and their union are still refusing to accept their bosses' tough new security regime, which officially came into force on Monday.

Unions are digging their heels in over a dispute over the "integrity package", with many of Immigration's 8500 public servants still fuming at the new requirements, which have been criticised as intrusive, unfair and over the top.

But a departmental spokesman says that consultaion has been going on for several months and that changes have already been made after feedback from the workforce and unions.

"The implementation of integrity and integrity related measures was advised to all staff last year; this included proposed dates for implementation of different sets of measures and related consultation periods," the spokesman said.

"In relation to the first set of policies, consultation opened on 17 December 2014 and closed on 23 February 2015.

"The Department has received considerable feedback from staff and the CPSU during this phase of consultation and has taken all feedback into account in the revision of the policies."

But despite the concessions, the main workplace union says much of the package of reforms remains unacceptable to many in the department and is now looking to make the dispute official.

The department's management, which says the new integrity measures are needed to bring Immigration's workplaces up to date with the modern dangers of corruption and security risks, has refused to delay implementation and is pushing ahead with the changes.

Immigration officials have been told they must complete an "organisational suitability assessment" if they want to work at the new merged agency combining Immigration and Customs.

The move by the Customs bosses, who are taking up many of the key posts at the top of the merged entity, comes despite all Immigration public servants already holding the "baseline" security clearances that are standard across the Australian Public Service.

But the new requirements go further, probing into past activities in the private lives of Immigration's bureaucrats and those of their families, friends and other acquaintances.

The changes come as part of a general workplace crackdown on Immigration public servants.

This also includes being breath and drug tested in their offices under the tough workplace regime that has been in force at Customs for several years.

The Community and Public Sector Union says it has won greater protection for employees' privacy and a "significantly pared-back declarable circumstances policy".

The union says workers will have to tell only the Australian Government Security Vetting Agency, and not their departmental bosses, if they change their religion or about other changes in their lives.

The tough new codes for dress and appearance have also been made "less onerous", the union says, but at a meeting last week a plea for more time to talk about other worries was knocked back.

"It is in our members' and the employers' best interests to delay implementation of the highly contentious polices so more work can be done between the parties to ensure the new requirements are more acceptable to staff," the union said in a bulletin.

"Members still have serious concerns about aspects of the other policies and we want to work with your employer, in good faith, to address those concerns.

"CPSU is deeply concerned that your employer has not agreed to delay implementation.

"This is disappointing as our preferred approach is to work collaboratively to achieve outcomes for our members."

The union has now lodged and official "notice of disputation" with the department, the first step in escalating the row to the point where it could go before The fair Work Commission.