ABARES has forecast winter crop production will increase by five per cent in 2021-22 to reach a record 58.4 million tonnes.
But the quarterly report found heavy rainfall in November across eastern states and South Australia will likely see a downgrade in quality for winter crops in some areas.
ABARES executive director Jared Greenville said recent rain in some parts of NSW may result in "localised losses, particularly for people on the floodplain".
The report also concluded heavy rainfall in November delayed the harvest of winter crops across some areas of NSW and Queensland.
Localised flooding in northern and central parts of NSW have also resulted in production losses for some growers, but that's not expected to significantly affect state totals.
Dr Greenville said quality "downgrades" were expected to affect the price though, particularly for wheat.
"It will really affect the value, less so the volume ... we're expecting to see some quality falls.’’
But Dr Greenville said overall wheat prices were "pretty strong" and the price "keeps on going up."
The new winter crop national record is driven by forecasts of record high production in Western Australia and the second highest record predicted in NSW and Queensland. Production in other states is also well above average.
The December forecast is a 6.6 per cent upward revision from the forecast ABARES published in the September 2021 edition of Australian Crop Report.
Record production of wheat, Australia's biggest winter crop, is expected to hit three per cent more than the previous record set in 2020-21, with 34.4 million tonnes forecast to be produced.
Canola is expected to produce 27 per cent above the record set in the previous year, with 5.7 million tonnes forecast, and barley is expected to produce its second highest amount on record, with 13.3 million tonnes.
With La Niña identified in November, a wet outlook for NSW and Queensland along with wetter than average soil moisture will also have an impact.
The report found it may lead to further quality downgrades and localised crop losses due to flooding, and also limited paddock access for winter harvest activities and summer planting programs.
The ABARES report expects the amount of summer crop planted nationally to increase by more than a third and reach 1.4 million hectares nationally.
That's put down in part to increased availability of irrigation water leading to more rice and cotton being planted.
Australian cotton production is forecast to increase by 78 per cent in 2021-22 to a near record of 1.1 million tonnes.