The ACT government has been unable to regulate groundwater use by the airport, which is on national land. But the oversight will be fixed and the airport will start paying for bore water from December this year.

An airport spokeswoman said in a statement to The Canberra Times the company had ''some'' bores ''for which we were granted approvals''.

''In that respect we are no different to other Commonwealth landholders in the ACT … there is no arrangement for a usage charge,'' the spokeswoman said.

But a Commonwealth Environment Department spokesperson said it had no record of licences for bores at the airport.

''The airport is not required to hold a groundwater licence … there is no requirement for the airport to report current water usage to the Commonwealth.''

Research fellow at the University of Canberra Institute for Applied Ecology Fiona Dyer said permitting one commercial business to access a finite resource without payment was an obvious mistake.

''The unregulated use of any resource is a problem, it needs to be addressed and changed,'' Dr Dyer said.

She said it would also impinge on the ACT government's ability to make an accurate sustainable water plan.

''There are a whole lot of equity issues as well in terms of why is one commercial operator able to access a resource free of charge when others have to pay for it,'' Dr Dyer said.

A spokeswoman for the ACT Environment Department said the airport would start paying for groundwater use on December 17 this year.

''When water resources on national land are handed over to the territory for management, it is expected that the airport will be licensed by the ACT government for groundwater use.''

They will be subject to an annual licence fee of $384.30 and a water abstraction charge of 25¢ per kilolitre for groundwater used.

In March 2010, Environment Minister Simon Corbell said ACT coffers would swell by $416,000 during the first financial year the government had control of all water registration and licensing in the territory, with $150,000 annually added thereafter.

The legislative changes necessary for the new powers were agreed to in principle in 2010.

The delay has cost the ACT government about $500,000 in forgone revenue.

Acting Minister for Environment and Sustainable Development Katy Gallagher said the Commonwealth began negotiations with the ACT in 2007 to ensure that water abstraction on national land and by Commonwealth bodies could be managed in accordance with the Water Act and on a consistent basis with all other water extractors in the ACT.

''The ACT government passed legislation in 2010 and the Commonwealth did not pass their legislation until 2013. When the Basin Plan was enacted, the impetus was there to make the legislative change,'' Ms Gallagher said.

''The ACT has not lost any revenue because it has not been the ACT's revenue to collect. The ACT will only have responsibility for water management on Commonwealth land from 17 December 2014.''

The 2010 Canberra Airport Environment Strategy makes reference to groundwater use and monitoring, but questions about bore water consumption and figures on use were not answered.

Calls to airport managing director Stephen Byron were not returned and a request for an interview with Mr Byron was denied.