Tests detected the potentially carcinogenic foam in the Indigenous community at Wreck Bay, near Jervis Bay. Authorities took four months to stop people using the contaminated waterway, documents released under freedom of information laws reveal.

The ACT government was warned in a August 2016 briefing that tests were needed urgently, and clear steps including closing the area would be agreed "as a matter of priority".

"Advice from the chief health officer is that if Mary Creek flowed through the ACT, the ACT government would already have closed this waterway to human contact, including swimming, drinking, foraging and fishing, enforced by signage and supported by communications directly with the community," the brief said.

ACT chief health officer Paul Kelly and the ACT's top bureaucrat, Kathy Leigh, pleaded for urgent action. But two early community meetings warning of the discovery attracted just 20 of the 200 residents.

For years, the poly and per-fluoroalkyl chemicals – known as PFOS and PFOA – leached from HMAS Creswell, the navy base next door, into Mary Creek, which runs through the Wreck Bay community.

PFOS and PFOA ingredients were in firefighting foam used for defence training from the 1970s and were phased out in 2004. The national environmental health standing committee has reported there is no consistent evidence that exposure to the chemicals causes adversely affects human health, but recent reports uncovered a possible link with cancer among residents of RAAF Base Williamtown, near Newcastle.

As further studies are undertaken, the Defence Department has restricted people from accessing the affected areas.

In documents released to Fairfax Media, Dr Kelly expressed frustration with the situation. In August 2016, Dr Kelly wrote to the Chief Minister’s delegate for Wreck Bay, urging that the investigation be progressed immediately and be prioritised above competing demands.

He noted that, quantitatively, the level of contamination and the population of the affected area was very similar to Williamtown, but the contrast in the way they had been treated was stark.

In Williamtown, an independent environmental consultant wrote a 3550-page report while, in Wreck Bay, there had been "a half-page email by a Commonwealth public servant on their last day on the job".

"I am getting increasingly uncomfortable about reputational risks to the ACT government and to me personally," Dr Kelly said.

The half-page email he referred to said that, through conversations with the Wreck Bay community, a federal Department of Infrastructure and Regional Development public servant had determined that children were known to explore the surrounding bush and creekbed of the contaminated area, and the creek was used occasionally, but not regularly, for food gathering and for swimming.

In Williamtown, land and water use was restricted after initial testing.

In Wreck Bay, testing of the area was not undertaken for more than a year, and the waterway was not closed for months after positive tests results.

In September 2016, Dr Kelly emailed Ms Leigh to advise that "based on the environmental results to date, Mary Creek should be closed right now to all human contact".

On October 4 and a week later, he again urged the government to close off the area and tell the community about the contamination.

"These results need to be urgently, transparently and carefully communicated to the community," he wrote.

Later in October 2016, a federal public servant emailed Dr Kelly to say the Wreck Bay board had been informed, and they were preparing warning signs to close the creek as a precautionary measure.

The email said the Wreck Bay Aboriginal Community Council had advised the government that Mary Creek was not a source of drinking water, and the community had been "well aware" of contamination in the creek since the 1990s.

An ACT government spokeswoman said it had consistently urged the Commonwealth to act collaboratively, openly and quickly to respond to PFAS in the Jervis Bay territory.

"The ACT has provided prompt and extensive public health advice when asked and stands ready to support Department of Infrastructure, Regional Development and Cities in any further investigations and response," she said.

"[The federal department] is the decision-maker for all health protection activities and the release of public health advice to the community. The ACT has no jurisdiction to take unilateral actions unless specifically engaged by [the department] to do so."

Wreck Bay is a secluded village on the coast near Jervis Bay. In 1986, the federal government gave the land to the Wreck Bay Aboriginal Community Council, which effectively acts as a body corporate for the self-regulating community.

The council's chief executive, Mal Hansen, declined a request for comment. "The board of directors of council have advised that, until the final test results have been received and examined, then it is premature to discuss this issue," he said.

The village is accessed by invite only. It is technically a Commonwealth territory managed by the Department of Infrastructure and Regional Development, however the ACT and NSW provide services.

This tangled web of decision makers proved complicated for the Department of Defence, who has responsibility for managing the contamination investigation. An old agreement permitted Environment Protection Agency testing on the land being undertaken from the 1990s, when separate contamination concerns were first raised, and this agreement was used to test the water initially.

However, in March 2017, the community’s board requested an independent expert to represent them in the new matter before any further samples were taken, which delayed a detailed environmental investigation for a year.

It was also noted that when faced with "near certain but undocumented" contamination in May 2016, not a single community member came to the open meeting to find out about the issue.

Another meeting held in October that year saw just two people attend. In March 2017, a meeting attracted 18 people.

A Department of Infrastructure, Regional Development and Cities spokesman said the community's wellbeing was "our absolute focus" and they would work with other deparments to provide advice and assistance.

"While these chemicals can persist in humans, animals and the environment, there is currently no consistent evidence that PFAS are harmful to human health," the spokesman said.