Water allocations for the Tindall Limestone aquifer in the Katherine region have been reduced.

For some water licence holders it is the third year running that their allocations have been trimmed.

Low-security water licence holders will only be allowed to draw 69 per cent of their annual allocation for the period from May 1, 2016 to April 30, 2017.

A low-security licence set aside for the Power and Water Corporation as a backup for Katherine has been reduced to zero.

Medium and high-security water licence holders have been allowed to retain 100 per cent of their allocation.

The changes mean 33,383 megalitres will be available to be extracted from the aquifer for the year.

The Department of Land Resource Management says just 30 per cent of water allocations were used in the last two years.

The department’s water resources division manager of policy and planning, Ian Smith, said low rain levels meant allocations had to drop.

“When we get a series of lower-than-average-rainfall wet seasons the recharge of the aquifer is reduced, that means the flows in the rivers that control the allocations,” he said.

“We may be in a low recharge, low runoff cycle and we should plan to see these sorts of allocations running into the future.”

There was some controversy in 2012 when departmental water allocation modelling was changed to consider only the past 30 wetter years, not the past 100 drier years as it had previously.

Mr Smith said the department was confident in its environmental science.

“Our confidence has really been bolstered by an independent review of that work,” he said.

“We always felt confident in that because the Bureau of Meteorology supports the use of the immediate past 30 years as an indicator of the likely immediate future.

“It is certainly not an indicator of an overall 100-year cycle, but our view is that we don't plan for the next 100 years we plan for the next 10, 15 years.

“The advice that we have from people like the BOM and other independent reviewers is that using that past 30 years is, for the next 10-plus years, best practice.”