Reservoirs in the Murray-Darling basin are now close to their lowest levels during the Millennium Drought and Tasmania is also facing "serious" issues", Dr Vertessy told Fairfax Media on Friday, his final day as the bureau's chief.

"Water shortage is a problem and climate change is going to be intensifying the drought and flood cycle," he said, noting that water demand is increasing. "Australia faces a really perilous water security challenge in the future." 

The bureau's boss bows out just days before the federal budget on Tuesday will reveal whether the government axes funding for programs set up under the National Plan for Water Security. Begun in 2007 by then prime minister John Howard. The 10-year, $10 billion program funded a range of water policies, with almost half going to the bureau.

The bureau now had "the world's best water information service", including precise stream-flow forecasting, that boasts a return on investments of between twofold and ninefold, despite the early stage of many projects, Dr Vertessy, a hydrologist by training, said. A drop in funding would result in a sharp reduction of services.

Funding constraints also hindered the bureau's ability to win its case to house climate researchers facing the chop at the CSIRO.

Facing criticism at home and abroad, CSIRO last week announced that it would instead form a special climate science centre of 40 staff under its Oceans and Atmosphere division. About 45 of the remaining 100 scientists in two key programs will lose their jobs and the future of those remaining is uncertain.

Dr Vertessy welcomed the centre's creation as an advance: "We were looking at the complete elimination of [the climate program] at one stage.

"Let's not sugar-coat it – CSIRO are diminishing their investments overall, they are probably halving them," Dr Vertessy said. "So it's really up to the rest of us now to work with them to build up the national capability to what it should be."

The need to boost global warming research was only going to increase. In Australia's case, the threats included lengthening and intensifying fire seasons, worse heatwaves and more intense storms.

"Unless we start slowing down our [greenhouse gas] emissions and really mitigating them completely in the next few decades, there's going to be a lot of environmental shocks to the planet," Dr Vertessy said. Human societies and ecosystems "are being pushed to the edge of sustainability".

The outgoing boss added that he "never fell hobbled" despite attacks on the bureau from some members of the Coalition, particularly during the Abbott government, and from climate change deniers who claimed the agency revised temperature data higher.

The bureau routinely used peer-reviewed processes to account for changes, such as shifts in locations of weather monitoring sites, to ensure data remained accurate.

"It's not too hard to imagine for conspiracy theorists that we're somehow rigging our data," he said. "The climate change trends we are reporting are absolutely robust."

The advance of technology promises ever more accurate weather prediction. The bureau will soon begin using a new supercomputer that promises 18 times faster data processing, and within three years, a 30-fold increase.

The resulting higher resolution capability would allow the bureau to scale forecasts down to 1.5 kilometres from 4 kilometres now, allowing an improvement in severe weather warnings.

Four cities, Sydney, Melbourne, Brisbane and Adelaide will also get more powerful radars over the next year, improving the ability to discern hail from rain, also providing improved warnings for the public.

Dr Vertessy, 55, said he would take a holiday after retiring before considering his next role after "running very hard for 14 years".