Australia's drought-hit regions are expanding in the lower Murray-Darling Basin as key climate influences in the Indian and Pacific oceans tilt towards drier conditions.

While June brought bumper rains to western parts of NSW, "a substantial area" of south-eastern South Australia and western Victoria has posted record-low rainfall over the past 12 months, the Bureau of Meteorology said in its latest drought update.

"Serious or severe rainfall deficiencies have been observed in parts of the southeast for various medium-term periods since late 2013, and for longer-term deficiencies for various periods under two years duration," the bureau said.

For some regions in the south-east, rainfall totals are the lowest since the 1914-15 drought, Blair Trewin, senior climatologist at the bureau, said: "That's an area that didn't do as badly as others during the Millennium Drought."

The southern wet season, which runs from April to November, has so far produced below-average rainfall for those areas in Victoria and South Australia, but also for the grain belt of Western Australia, the bureau said.

Measured over the longer term, such as the past 33 months, the drought-affected regions involve a much larger area, covering most of inland Queensland.

While June was relatively dry for Victoria - state-wide totals were 30 per cent below average – NSW fared much better. A complex low-pressure system that formed mid-month helped lift rain totals to 26 per cent above average, with places such as Bourke recording their best June falls since 1948.

Soil moisture

While upper-layer soil levels received a boost, lower levels remain on the dry side for many eastern parts of the nation, the bureau's data shows.

 The dry conditions may extend further, with the bureau forecasting below-average rainfall for the July-September period for most of Victoria and the eastern half of NSW and Queensland.

One influence is the intensifying El Nino in the Pacific. The event, in which rainfall patterns tend to shift eastwards as the normal easterly trade winds stall or reverse, may be a particularly strong one, climate specialists say.

Another is the so-called Indian Ocean Dipole – which gauges relative warmth between the western and eastern parts of the ocean. The bureau's models indicate the IOD will become positive in July, which would tend to mean less moisture streaming over the Australian continent during the winter and spring and less rainfall in the south-east as a result.

Perhaps even more important is the strengthening of the sub-tropical ridge over the continent, which has pushed cold fronts further south, Dr Trewin said.

Towns such as Mount Gambier in south-eastern South Australia could normally count on 20-25 days a month of rain during winter, each bringing only a few centimetres of rain, but not this year, he said.

El Nino impact

The NSW government indicated it is preparing for lower farm output in its budget released last month. Its reports included the following chart showing how output tends to track changes in the Southern Oscillation Index – one gauge of El Nino activity.

 Jeremy Buckingham, the Greens NSW agriculture spokesperson, said the Nationals should pay heed to the longer-term signals and drop their general denial that climate change is making natural variability worse.

"Billions of dollars in farm productivity are being lost to the detriment of regional economies due to drier conditions and climate change will only make this worse in the years ahead," Mr Buckingham said.