The dam at Upper Stranger Pond, which sits between Isabella Drive and Drakeford Drive, was drained without authorisation earlier this month.

Thousands of native Australian fish were introduced to the pond in January to replenish their numbers after the water was cleared of introduced carp.

A spokesman for the City Services directorate, which oversees Canberra's drains and dams, confirmed it had been drained by a contractor before it had been drained again without authorisation.

But Canberra Fisherman's Club president Glen Malam said the government needed to be more clear about when the pond had been drained by the contractor.

He also said the government should restock the native fish "urgently" before they became food for carp in the nearby Lower Stranger Pond.

The government cleared 2.6 tonnes of dead carp, killed by draining Upper Stranger Pond, in April last year. It then released 1000 Murray cod and 1000 golden perch fingerlings.

Carp are considered a pest and feast on juvenile native fish, carry disease and, because they are bottom feeders, constantly stir up sediment in water bodies.

The City Services spokesman said the government wouldn't need to replenish the native fish stocks because they would have moved to Lower Stranger Pond and grown to about 15 centimetres.

But Mr Malam said this put the fish at risk of being food for the carp living in Lower Stranger Pond.

"It seems a crying shame to drain the pond and flush these young fish into Lower Stranger Pond," Mr Malam said.

"One also wonders if the contractor undid the wrong valve on the wrong dam. It does beggar belief that someone could just open the plug."

The City Services spokesman said the draining was part of planned works at Isabella Wetlands and security measures were being upgraded at the valve.

"It worries me that all of our lakes have open access to be drained overnight by someone with malicious intent or just a very poor sense of humour," Mr Malam said.

Mr Malam inspected the valve at the dam on Friday and said it would be very easy to for someone to open it with an adjustable spanner.

When provided the response by the City Services spokesman, Mr Malam said he wanted a more detailed explanation from the government.

The loss of the native fish would be a great shame considering the effort the government had done to improve the health of Canberra's waterways, he said.

"The plan was a very wise one: to clean up the dam, remove the carp, install snags and restock the native fish," Mr Malam said.

He said the fingerlings needed time to become a good stock of large native fish before the carp returned.

A previous version of this article stated the carp in Upper Stranger Pond were killed by an introduced herpes virus. This virus has not been approved for use in Australia at the time of writing.