NICOLA Sturgeon admitted there has been a "lack of clarity" around new coronavirus rules as she told businesses unsure of their position to close.
The First Minister made the comments just hours before a two-week hospitality shutdown came into force across central Scotland.
Pubs and restaurants have closed, but cafes have been told they can remain open even if they are licensed, as long as they don't sell alcohol.
However this sparked widespread confusion over the definition of a cafe, as licensing laws make no distinction between cafes, restaurants and bars.
Ms Sturgeon was accused of overseeing a "complete shambles".
During her regular briefing, she said new regulations - published just minutes before she stood up to speak - define a cafe as an establishment where the "primary business activity...is the sale of non-alcoholic drinks, snacks or light meals".
She warned restaurants cannot "decide to stop selling alcohol, become cafes and stay open" as that would "undermine the purpose of these restrictions".
She said: "If a premise is in doubt, they should close, unless an environmental health officer tells them that they think they fall within the definition.
“Now, if cafes are finding this difficult, then the only alternative we will have is to say anybody with a licence should close."
Ms Sturgeon said cafes are being exempted to "give people, particularly those who might be living alone and also working from home, somewhere that they can still meet a friend for a coffee and a chat".
She said ministers had realised the new rules created an anomaly for cafes with an alcohol licence.
She said: "What I announced the other day would have forced these cafes to close, and in some areas, particularly rural areas, they might be the only cafe in the village.
"So we decided to try to resolve this in a very targeted way.
"And in the 24 hours that we've been doing so, I readily accept that that has resulted in a lack of clarity.
"But sometimes that's the price we have to pay right now for trying to be as flexible as possible.
"It would have been much easier, and would have given much greater clarity, just to stick to the position yesterday that cafes with a licence have to close."
She said businesses with doubts or questions should discuss these with local environmental health authorities.
However she later said: "We are defining this as well as we can.
"But if any premise thinks they want greater clarity, my only advice I can give is to close."
Elsewhere, she repeated: "What I'm about to say is hard and tough, and I recognise that.
"But if you are a business asking yourself the question – am I really a restaurant? - then perhaps you should be on the side of closing for the next two weeks."
The First Minister previously unveiled sweeping restrictions including the 16-day closure of licensed premises, such as bars and restaurants, in central Scotland from 6pm today.
The shutdown applies to Greater Glasgow and Clyde, Lanarkshire, Ayrshire and Arran, Lothian and Forth Valley.
Elsewhere in Scotland, alcohol will be banned inside bars and restaurants and all indoor hospitality venues will have to close at 6pm.
The new measures are set to be in place from 6pm to October 25, inclusive.
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