The Scottish Conservatives said the checks would be “nothing short of economic vandalism”.
It came as a leading economic research institute said the First Minister’s economic prospectus left “some of the most difficult questions unanswered”.
Ms Sturgeon launched the latest in a series of papers setting out the Scottish Government's updated case for independence on Monday.
Focused on the economy, the paper said an independent Scotland would apply to rejoin the EU and the Scottish Government "would put in place measures to smooth any checks required as a result of Brexit on goods moving to and from England and Wales".
The document said physical customs checks “would likely only be undertaken on the two main trunk routes between England and Scotland or at rail freight terminals”.
Ms Sturgeon later confirmed the trunk roads referred to would be the A1 and A74(M), which becomes the M74.
The Tories said almost 60 per cent of Scotland’s exports in 2019 were to the rest of the UK. The statistics for 2020, which were published this week last year, have yet to be released.
Scottish Conservative finance spokeswomen Liz Smith said: “Nicola Sturgeon is clueless about the impact a hard border would have on businesses and communities right across Scotland.
“Her latest wafer-thin economic case for independence had no answers on what this would mean for our border communities, the people that routinely travel across the border every day and Scottish businesses who trade with the rest of the United Kingdom.
“Nicola Sturgeon is putting her own selfish obsession of relentlessly pursuing independence rather than outlining the economic costs of what a hard border would mean.
“That is a complete dereliction of duty. Nicola Sturgeon should urgently reveal the SNP’s own economic modelling on a hard border and the reality of what it would mean in practice.”
Meanwhile, the Fraser of Allander Institute at the University of Strathclyde said Ms Sturgeon’s economic prospectus “answers some questions, but still leaves some of the most difficult questions unanswered”.
Ms Sturgeon wants to hold a second referendum on October 19 next year.
Marking one year to go, she said: “The Scottish Government’s renewed prospectus for independence is making the case for an economy that works for everyone – dedicated to helping people live happier, more fulfilling lives. And the more questions we answer about Scotland’s future under independence, the more the questions pile up for those advocating continued Westminster control.
“If Scotland were independent right now, there is no chance that we would look at today’s UK and believe it was in our interests to be ruled by Westminster. We would never choose to be in a travesty of a partnership, which routinely ignores our democratic wishes, a country with an under-performing economy and growing inequality – in short, a political system which is dragging us down the wrong path.
“Independence is no guarantee of success, but it is a guarantee that we will get rid of Tory governments we don’t vote for, for good – and no one will ever take better decisions about our future than the people living here.”
She added: “A year today, I want people in Scotland to be able to go the polls and choose that better future.”