Lower branches of the popular, long-standing Lilly Pilly trees in reach of small hands were due to be cut down but the school wished to take a "zero risk approach" and the decision was made to remove the trees entirely.

The trees and creeks are contaminated with poly and per-fluoroalkyl chemicals – known as PFOS and PFOA - which leached from a nearby Defence base.

The chemicals were ingredients 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.

An ACT education directorate spokeswoman said the trees, which produce fruit between December and January, are generally not consumed and "would pose very little health risk, unless very large quantities of the fruit are eaten".

"Low levels of PFAS were found in a small number of samples of fruit from the trees," the spokeswoman said.

Meanwhile, two years after one creek used for fishing and swimming was closed to all contact in Wreck Bay, an Indigenous community near Jervis Bay, three more creeks in the area have been found to be contaminated.

Seafood in Summercloud Creek, Captains Lagoon and Flatrock Creek tested positive to elevated levels of toxic chemicals.

ACT Health through the Department of Infrastructure has warned residents against eating fish or shellfish from the locations.

Earlier this month, a community bulletin sent to Wreck Bay residents stated the department would work with land managers in the Jervis Bay territory to erect signs at the newly identified contaminated sites as a precautionary measure until Defence’s human health risk assessment of the area has been finalised. The report is due by the end of 2018.

While seafood consumption guidelines are in place for waters at nearby HMAS Creswell, specific guidelines are not in place for the Indigenous community.

An ACT Health spokesman said despite undertaking the testing, the ACT government was not responsible for public health advice and consultation in the Jervis Bay Territory.

"This is the jurisdiction and responsibility of the Department of Infrastructure and Regional Development and Cities. ACT Health has provided advice to DIRDC at its request. The DIRDC is responsible for taking appropriate action to protect public health based on information it receives, including releasing advice," he said.

Issues of jurisdiction have plagued the Defence investigation in Wreck Bay, a self-determining community on Commonwealth land administered by the Department of Infrastructure with services provided by NSW and the ACT.

In documents released under freedom of information laws, the ACT government's Jervis Bay Territory liaison delegate agreed in May to accept an offer from the NSW Environment Protection Authority to undertaken consumption calculations to assist with forming advice for the community.

The email states that the authority advised the ACT government that based on an assessment of the results from Flatrock Creek and Captains Lagoon, which flow into Jervis Bay near Hyams Beach and Green Patch, that "we had the same potential issues as Currumbene Creek". Dietary advice for six species of fish in Currumbene Creek, near HMAS Albatross at Nowra, was issued in May.

That advice followed the Environment Protection Authority's similar warning over the Shoalhaven River in November 2017.

The Department of Defence, which is managing the contamination program, maintains that no detectable contamination has been found in drinking water in the area.

Member for Fenner Andrew Leigh visited Wreck Bay earlier this month for the first time in a year to discuss the contamination with the school and the wider community.

"Worryingly, there is some contamination on the school grounds, and the school leadership team is discussing the appropriate way to address it," Dr Leigh said.

“I will shortly write to the minister for an update and will continue to engage with the community about PFAS contamination.”