In 2012-13, the average farm business income was £30,000, a drop of 34% on the previous year.
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 in 2012-13.
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."
Lowland cattle and sheep farms, and cattle and sheep farms in less favoured areas, saw their incomes more than halved, it added.
The report, which was based on findings from the Farm Accounts Survey, said livestock costs had "contributed the most to the decline in profitability of Scottish farm businesses in 2012-13".
It said the amount farmers spent on feed for livestock increased by an average of £6,000 last year, rising to £37,000.
But half of all farms received extra income from other sources in 2012-13, with farmers turning to activities such as tourism and recreation, 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.
Rural Affairs Secretary Richard Lochhead said: "These figures confirm what we already know - that the 2012 season was extremely tough going for almost all farming sectors in Scotland and across the UK.
"All the indications are that 2013 was a much better year for Scottish agriculture, as shown in the Total Income from Farming 2013 statistics, and my expectation is that this will be reflected in next year's Farm Business Income report."
Mr Lochhead 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.
"I look forward to seeing similar results from Beef 2020 Industry Group led by Jim McLaren, the Scottish Government's Poultry Plan and our significant investment in the infrastructure supporting Scotland's pig industry. However it is key that the UK Government also take action to support Scottish livestock by approving our proposals for increasing coupled support."
But 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."