Revenues fell to USD 60 million (71 million euros, USD 79 million) in the 2015-2016 financial year from 1.8 billion pounds in the previous 12 months -- a 97-percent drop due to the dip in oil prices, the data showed.
Scotland's public deficit also rose to 14.8 billion pounds, up from 14.3 billion pounds in the 2014-2015 financial year.
"The lower oil price has, of course, reduced offshore revenues, with a corresponding impact on our fiscal position," Scottish First Minister Nicola Sturgeon said.
The Scottish government yesterday warned of the heavy financial burden from Britain exiting the European Union, claiming an annual cost to the economy of up to 11.2 billion pounds.
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At the same time however, the cost could be much lower at 1.7 billion pounds a year in lost gross domestic product (GDP) by 2030, it added in a statement.
"This paper shows, in the starkest possible terms, the potentially huge cost to Scotland of being taken out of the European Union and the single market," Sturgeon said.
Following the shock outcome of the June 23 referendum, Sturgeon earlier this month announced plans for increased infrastructure spending to boost the Scottish economy.
The devolved Scottish administration said it would invest an extra 100 million pounds on health and other infrastructure projects in Scotland this year.
Prime Minister Theresa May must now decide when to activate Article 50, which formally triggers the country's departure from the European Union.
Sturgeon campaigned for Britain to stay in the European Union and has said she wants to preserve close EU ties even if Britain leaves, which could include a new bid for independence.