Dr David Jones from the Bureau of Meteorology said Australia was facing a "substantial" El Nino event this year, the first since 2009-2010.

"This is a proper El Nino event. This is not a weak one or a near miss like last year," he said.

Effects of El Nino include increased risk of drought, increased daytime temperatures in southern Australia from winter onwards and an earlier and more extreme fire season.

Dr Jones said farmers faced a tough growing season.

"We see increased frost risk in winter; that's because the soils are dry and there's less cloud cover," he said.

"The typical pattern we would anticipate in the coming months to two seasons is the emergence of below average rainfall conditions."

Regions already suffering through drought or near-drought conditions such as central Victoria will face a continuing deterioration of seasonal conditions. The effects of El Nino events are most keenly felt in the eastern states. 

The bureau's Dr Lynette Bettio said while likely, it wasn't certain drought conditions would continue to worsen. 

"El Nino events aren't always associated with drought in Australia but they are often associated with drought," she said.

She said the lack of rainfall during summer coupled with the forthcoming El Nino conditions meant farmers were facing very low soil moisture levels.

Department of Economic Development, Jobs, Transport and Resources Epsom seasonal risk agronomist Dale Grey said rainfalls at the weekend were not enough to give farmers the seasonal break they urgently needed.

Areas to the north and west of Bendigo received only about 5mm, while areas south of the city fared slightly better, he said.

"We are in desperate need of something in the order of 25mm to get the season kicked off," he said.

Mr Grey said the smattering of rain could have negative effects for farmers who had chosen to dry sow.

"The rainfall on the weekend made the moisture content a bit dangerous," he said.

"Seeds might strike but they may not have enough to live on."

He said farmers were making decisions now about what, if anything, they would sow.

"Given the low soil moisture, the western regions will probably cut back on canola," he said.

Hardier crops such as barley and oats, which can deal with tougher seasons, are likely to be in favour.