Yesterday the Department of Conservation confirmed it had raised "concerns" about the working relationships in Ms Allan’s office more than a year ago and one staffer had left her office early as a result. Other government departments had also raised concerns.
The news broke soon after Ms Allan posted on social media that she had taken mental health leave last week because of "personal circumstances" and work pressure.
It is understood the mental health leave is not connected to the issue of her office environment.
The news forced PM Chris Hipkins to speak about the issue from China, where he had just met with China’s Premier Li Qiang.
National’s public service spokesman Simeon Brown said the allegations raised serious questions that Ms Allan and Mr Hipkins needed to answer.
However, Mr Hipkins said there had been no formal complaints lodged with his office against Ms Allan, and earlier concerns were dealt with without the need to escalate them. He had not known about the earlier concerns, which pre-dated his time as Prime Minister, but became aware of it recently after inquiries were made.
He did not believe Ms Allan’s mental health leave was related to that and said he supported ministers taking a break when they needed to.
In a statement, Ms Allan said she had "great working relationships with my office crew".
"Like in many offices and workplaces, there are sometimes challenges with working relationships and the Beehive is no different. I value my crew and I have always been clear that I have high expectations of senior public servants, as I do myself."
Earlier, Department of Conservation director-general Penny Nelson confirmed in a statement that she became aware of concerns about the "working relationships with the minister in the office, and that it was not running as smoothly as it might". It had happened more than a year ago.
"One person chose to end their secondment early due to the working relationships in the office. Accordingly, I had discussions with my colleagues, including from Internal Affairs, which manages Ministerial Services, regarding support in the office.
"No further concerns were subsequently brought to my attention, and I understand relationships improved."
Stuff reported that other concerns were raised by the heads of Emergency Management and the Ministry of Business, Innovation and Employment.
Ms Allan’s post on social media yesterday said she had returned to work after a period of leave because she was "struggling with mental health and wellness" over the past few weeks.
"Triggered by personal circumstances, as well as other external things — even things like the cyclones having such a massive impact on our entire region," said Ms Allan, who is responsible for justice and regional development, and as East Coast MP is based right in the heart of areas hammered by successive cyclones and weather events this year.
"Sometimes things accumulate, and I hit a wall a few weeks ago."
Ms Allan said she had taken a week off to get some help to get back on track. She also urged others struggling to reach out for help.
Alongside managing the impacts of the cyclones, Ms Allan has in recent months faced several political scandals.
In April, she had to apologise after criticising RNZ and its treatment of Māori staff at a private event hosted by the broadcaster.
Shortly after, 1News revealed then-Race Relations Commissioner Meng Foon had donated to Ms Allan’s political campaign. While it came before Ms Allan was Justice Minister, after she became minister she had responsibility for Human Rights Commissioners, and should have declared the potential perceived conflict with the Cabinet Office.
Ms Allan has also faced challenges in her personal life while an MP. In early 2021 she was diagnosed with cervical cancer and took time off for chemotherapy.