Australia faces a "perilous" water security future from climate change even as the Turnbull government eyes budget cuts to water programs and CSIRO halves climate investment, Rob Vertessy, the outgoing head of the Bureau of Meteorology, says.

Reservoirs in the Murray-Darling basin are now close to their lowest levels since 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 $450m going to the bureau.