The agency overseeing Australia’s almost $400bn acquisition of nuclear submarines is facing a staff morale crisis and the threat of an external review of its operations, with a key deputy director leaving after just a year.

The Australian Submarine Agency, or ASA, was established 17 months ago to oversee submarine purchases under the Aukus pact but Guardian Australia understands it has become the subject of growing government concern about its priorities, governance and leadership.

Last month the agency’s deputy director-general responsible for policy and program implementation, David Hallinan, quit and was reassigned to a senior position within the department of defence.

Guardian Australia understands Hallinan left, having held the position for a year, after he tried to raise concerns about the agency’s operations and was dissatisfied with the response.

The defence minister, Richard Marles, is understood to have raised concerns about the state of the agency with the ASA director-general, Vice-Admiral Jonathan Mead, including the possibility of ordering a review of its priorities and how it operates.

The findings of the annual Australian Public Service staff census, published last week, ranked it second worst for staff wellbeing and support of all 104 departments and agencies across the federal bureaucracy.

The responses of 397 ASA staff, among a workforce of 502, also ranked it close to the bottom on internal communication. It scored significantly below the public service average on enabling innovation and also in the bottom half on leadership and employee engagement.

Of the ASA respondents, 70% said they were significantly or slightly overworked, 42% reported being stressed often or always and 38% said they felt burnt out – increases on last year’s responses and mostly higher percentages than for other comparable agencies.

Just under a third of the agency’s workforce rated it negatively on its senior executives working as a team and on attitudes to failure as a necessary part of innovation. Almost 40% rated it negatively on internal communication and 36% marked it down on managing change.

A spokesperson for Marles had no comment but directed Guardian Australia to the minister’s remarks at a Submarine Institute of Australia conference on 5 November.

“It’d be unlikely for me to be sitting here saying everything is perfect– everything is not,” Marles said at the time.

“But a lot is, and I think we’re aware of where we need to make up ground. And so I do fundamentally have a real sense of confidence that this program is going in the direction that it is, and part of that is based on the fact that we really are trying to interrogate ourselves, hold ourselves to account about where more needs to be done.”

Hallinan declined to comment and referred questions to defence, which also declined to comment on Hallinan’s new position or the reasons for his job change.

“It would not be appropriate to comment on any individual’s circumstances,” the department said in a statement.

The agency’s executives – including Hallinan – attended the Senate’s defence and foreign affairs estimates committee hearing on 6 November as required, but were not called to answer any questions because the committee ran out of time.

The Coalition and Greens have been pressing the government to schedule a spillover hearing to question the agency before Christmas.

In response to questions from Guardian Australia, the ASA highlighted other more positive findings in the staff survey, including that it had a highly engaged and committed workforce willing to go “the extra mile”.

“This is a tremendous effort for a newly established Agency,” a spokesperson said in a statement.

“The ASA has transitioned from a Taskforce in a large Department to a growing Agency that is working to deliver the single biggest investment in defence capability in Australian history.”

It said the Australian Public Service Commission had indicated that the results were “common for newly established agencies”, that its leadership had consulted staff after the census results were released and developed an action plan to address them.

“There are of course areas of improvement, including in change management and internal communications and we recognise this.”

The opposition defence spokesperson, Andrew Hastie, called the census results “troubling”.

“Especially for a agency that’s only just turned one year old,” Hastie said. “The Albanese government’s lack of leadership, lack of clarity and lack of resolve are on stark display as 56% of ASA employees aren’t clear about what they are meant to do.”

The Greens defence spokesperson, David Shoebridge – a strong opponent of the Aukus submarine deal – said it was not surprising the agency appeared “rudderless” based on the survey results.

He said senior leadership were “unable to explain the ASA’s strategic direction” and highlighted “chronic communication issues” felt by staff.

“What is worse for people trying to work at the ASA is that there is no reasonable prospect of them having any submarines in their professional lifetime.”

The Aukus pact involves Australia buying at least three and possibly as many as five US designed and manufactured Virginia class nuclear-powered submarines, to be commissioned in the 2030s.

Ahead of the acquisitions, from 2027 at the earliest, Britain and the UK plan to establish a rotational presence of one Royal Navy Astute class submarine and up to four US navy Virginia class submarines at HMAS Stirling, a Royal Australian Navy base near Perth.