Border delays and a plummeting currency are also likley – with two-thirds of firms fearing that there won’t be a deal in place by the 29 March deadline.
It could threaten the viability of some firms, with competitiveness and profitability set to be hit, according to the survey by EY.
Almost a fifth (18 per cent) of businesses said they did not feel ready for Brexit at all, although the majority (74 per cent) said that they had taken steps to prepare.
Only 8 per cent said they felt fully ready for Brexit.
Scotland’s Finance and Economy Secretary, Derek Mackay, called on the UK government to rule out a no-deal Brexit which he said would have “devastating consequences”.
He said: “This report demonstrates the costs to Scotland of a Brexit we did not vote for and demonstrates why a no-deal Brexit must immediately be taken off the table by the UK government.
“On top of the damage it is clearly causing to Scottish businesses, Brexit, in whatever form, will cost jobs, make people poorer, damage our society and undermine the democratic decision of the people of Scotland to remain in the European Union.
“The UK government must now take urgent steps to rule out a no-deal Brexit, which threatens to have devastating consequences for jobs, businesses and communities, extend the Article 50 process and hold a second referendum on EU membership.”
Businesses also raised concerns that Brexit would reduce access to talent at all wage and skill levels, with the food and drink, financial services, life sciences and creative sectors particularly affected.
They are also concerned that tariffs and non-tariff barriers will disrupt the frictionless and tariff-free movement of goods between Scotland and the EU.
The report states: “Tariffs and non-tariff barriers will clearly make it harder for Scottish businesses to trade with the EU, and will likely reduce the volume of trade.
“The sectors that appear most vulnerable include food and drink, chemicals, life sciences and other manufacturing sectors.
“Impacts are likely to be felt quickly, although longer term there may be opportunities to explore alternative international markets and rebuild domestic supply chains.”