Two eucalyptus trees with significant value to Canberra's Indigenous community have been "wrongly" cut down, according to Government documents.

Key points: Scar trees are of "cultural significance to Traditional Custodians"

Scar trees are of "cultural significance to Traditional Custodians" Contractors removed two scarred trees in Canberra's south in error

Contractors removed two scarred trees in Canberra's south in error There is no way to prosecute scar tree destruction in the ACT

The two trees in the suburb of Wanniassa both bore deep scarring from where canoes had likely been carved hundreds of years ago.

One of the trees has been relocated, but the second — affectionately known by locals as the Spook Tree — has been destroyed.

"Scar trees are done by our ancestors, but also there are stories behind them, a spiritual connection," Ngunnawal elder and traditional custodian Tyronne Bell, who runs cultural tours of scar trees around the ACT, said.

"When one of them gets destroyed, part of us gets destroyed with it."

Trees removed, turned to mulch

One of the scarred trees in Wanniassa, after being cut down.

Access Canberra investigated the "destruction" of the Spook Tree, which was cut down and mulched in April 2017, ultimately finding it had been mistakenly removed as part of a larger tree removal program.

"The contractor undertaking the clearance had sought advice from the Conservator of Flora and Fauna, in line with standard process prior to removing any trees, and it was identified as a tree not to be removed," ACT Conservator Ian Walker said.

"Unfortunately an error by the contractor saw the tree wrongly removed … the contractor notified the ACT Government straight away and expressed their regrets."

The scarred tree at the Wanniassa District Playing Fields was another tree of 'cultural significance'. ( National Library of Australia: Jon Rhodes )

Despite the mistake, the Government decided not to pursue the contractor through what would be an "expensive prosecution".

But the circumstances surrounding the felling of the other scarred tree are less clear.

The investigation into its removal is ongoing, but the ABC understands it was intentionally removed around the beginning of 2017.

Its trunk has been saved, and Aboriginal organisations are being consulted on what can be done to conserve it long term.

Community says there are 'no excuses'

Mr Bell called for tougher penalties to bring the ACT into line with NSW, where fines can be as much as $1.5 million for scar tree destruction.

In the ACT, there is currently no system in place to issue fines or repair orders without prosecuting breaches through the courts.

"People before they cut a tree down they should get in contact with the Aboriginal Heritage Unit," Mr Bell added.

"Some people go and cut these trees down because they're not educated, but some people know it's a site and they knock it down anyway because they're a developer and they need to get something built."

Ngunnawal elder Tyronne Bell points out a scar tree on one of his tours at Mount Majura. ( ABC Radio Canberra: Penny Travers )

Inner South Community Council member Nick Swain wrote online that the historical society had questioned the Planning Minister over the safety of other protected trees.

"There are no excuses for this! What practical protection does the Heritage Register provide to these special cultural objects?", he wrote.

In briefing documents to the Environment Minister, the Environment directorate advised it was exploring ways to educate the community on identifying scarred trees.

"The ACT Government recognises the importance of Aboriginal scarred trees to our region's heritage," Mr Walker said.

"Scarred trees are of cultural significance to Traditional Custodians, and they are also of archaeological significance as they can provide an enormous amount of information on past Aboriginal activity and use."

Mr Walker said in February that Environment Minister Mick Gentleman had asked the directorate to explore the introduction of on-the-spot fines and repair orders "as a matter of urgency".

He said that work was expected to roll out this year.