Rising costs for items such as feed, the wettest June on record two years ago and the biting cold and snow that followed early last year have hit farmers in the pocket.
Crops were ruined by too much rain, machinery could not be used and cows could not graze in sodden fields. Livestock also suffered during last year's snow.
Shoppers also face two more years of inflated prices for groceries after the "disastrous" harvest of 2012.
One farmer said yesterday he believed the impact at the supermarket would be slight but could continue for another two years.
The new figures show that the average farm business income was £30,000 over 2012-13, a drop of 34% on the previous year.
The average income is farmers' lowest for four years.
When cash from grants and subsidies were excluded, the average farm made a loss of £16,000 last year, according to data from Scotland's Chief Statistician.
A total of one in five farm businesses made a loss.
However, half of all farms received extra income from other sources in 2012-13, with farmers turning to activities such as tourism and recreation - such as hiring out cottages for trekkers - taking contracting work and hosting mobile phone masts on their land.
Of these, it was mobile phone masts and the processing and retailing of farm produce that generated the greatest average incomes, according to the report.
Small to medium scale wind turbines were also cited as new form of income.
Tom French, a dairy farmer in Crawfordjohn, South Lanarkshire, said: "It will make a slight difference to the cost of some (produce) but not a huge difference. It is going to take three or four years to recover."
Jonnie Hall, of the National Farmers' Union Scotland, said: "The influence of the weather over 2012 and 2013 had a huge effect on input costs and yields for farmers in Scotland and the knock-on effect to incomes, while deep and painful, are not a surprise to those in the industry. These figures simply underline the value of ongoing support to active producers."
The report revealed: "With the exception of general cropping farms, all farm types in Scotland have seen a decrease in income in the latest year, with cereal and dairy farms being most severely affected."
It said the amount farmers spent on feed for livestock increased by an average of £6000 last year, rising to £37,000.
Rural Affairs Secretary Richard Lochhead said: "All the indications are that 2013 was a much better year for Scottish agriculture."
However, he said it was particularly concerning that both lowland and upland cattle and sheep farms had suffered "such a significant fall in income".
He added this "highlights how important it is we have the right support in place for our farmers and crofters in the next CAP (Common Agricultural Policy)".
He also highlighted the rising number of dairy cattle in Scotland, saying: "This is a welcome sign of confidence in this sector, which remains one of the most profitable in Scottish farming, and which will provide a solid platform for taking forward the Dairy Growth Strategy commissioned by the Scottish Government."
Liberal Democrat Tavish Scott said the Scottish Government "should be addressing the financial challenge facing Scottish agriculture" instead of "obsessing about independence".
He added: "Farmers and crofters want a government on their side, not one that spends every day working out how to separate Scotland from its largest export market.
"These stark figures show what needs to be addressed especially as crucial decisions over CAP are taken by the SNP Government."