Consumers are warned to expect fruit and vegetable shortages at supermarkets for another six weeks, with supply expected to be back to normal by September.
Acting chief executive of the National Farmers' Federation Ash Salardini said empty shelves can be directly linked to poor weather earlier this year in parts of northern NSW and Queensland.
"During the winter months, that's where we get most of our fruit and veg ... in four to six weeks the rest of Australia should have some of those fruit and veg come online," Mr Salardini told AAP.
"We should have a lot less availability issues in four to six weeks' time."
However, he warned that once more fruit and vegetables became available there could still be supply chain disruptions while getting them to market.
In a message to shoppers on Thursday, Woolworths warned of extreme shortages of fruit and vegetables.
The seasonal outlook said zucchinis, green beans, tomatoes, lettuce, spinach, spring onions, Asian leafy greens and berries would remain in short supply until July.
Poor weather has also affected fresh herb stocks, and availability is not expected to improve until August.
Woolworths general manager of fruit and vegetables Paul Turner said many growers were still experiencing the effects of heavy rain from earlier in the year.
"This has pushed back the planting and harvesting of crops, with reduced availability continuing to be exacerbated by cooler temperatures and low levels of sunlight," he said.
Coles has reported low supplies of berries, lettuce, beans, tomatoes, broccoli and herbs due to the devastating floods in northern NSW and Queensland, resulting in higher prices.
"Produce pricing is subject to supply but as soon as volumes recover, we will be working hard to get prices down for our customers as quickly as we can," a company spokesman said.
In southeast Queensland, where the cold has resulted in undersized lettuces, Coles is selling two smaller lettuces for the price of one.
"These lettuces haven't fully grown due to the extremely cold weather," the spokesman said.
"The initiative allows growers in the Lockyer Valley to use some of the iceberg lettuce crops that have been impacted on by the recent wet weather and will improve availability for customers."
Another of Australia's major supermarkets ALDI has also had supply issues.
""We continue to support our local growers and hope that growing conditions become more favourable to support improved yields and ongoing sustainable production," a company spokesman said.
AusVeg spokesman Tyson Cattle told AAP although supply may return to normal in coming months, he expects the cost of fruit and vegetables will remain high.
"All growers cost of production inputs have gone up considerably so we won't go back to previous pricing levels, given that growers' costs have increased ... by 35 to 40 per cent," he said.