Natalie James told a Senate estimates committee on Tuesday she wanted to respond to reports in the Australian newspaper that said more than 70 per cent of her staff "disconnected from the office" in 2023.
The secretary clarified that as of December 31, 2023, one-third of staff at the department regularly work from home for an average of 1.9 days per week.
In total 1298 employees have a WFH arrangement.
"I'm proud of the flexible working arrangements we have in my department," Ms James said.
"To suggest that my people are disconnected from the office when they are working from home could not be further from the truth. They are the opposite of disconnected," she continued.
"They are about as wired into the matrix as you possibly could be."
The secretary said she had contacted the newspaper to correct the reporting, which had included the number of people who worked from home on an ad hoc basis to justify the higher figure.
The department is responsible for drafting the new "right to disconnect" laws that passed parliament on Monday.
Under the workplace reforms, employees will have the right to ignore unreasonable calls and emails outside of their rostered shifts.
The right to disconnect was part of a broader package of measures, which also included greater rights for gig workers, as well as provisions for casual employees to transition into part time or full-time employment.
"The new laws will be a prompt for us all to be having conversations with our people... to respect boundaries and wellbeing," Ms James said.
Workplace Minister Tony Burke said the measures were long overdue.
"Workers, as they've gone to having their own mobile phone over the last decades, have now waited too long just to know you don't have to constantly be on call," he told parliament.