Scottish shoppers face higher prices at John Lewis department stores if the country votes for independence next week.
This comes after the head of DIY giant B&Q said Scots could be charged more in an independent Scotland, and the energy industry signalled that their bills could go up too.
John Lewis Partnership chairman Sir Charlie Mayfield said he would "regret" any move which damaged the retailers' partnership model. "We have got a thriving business in Scotland, with nine shops, a contact centre and over 3,000 partners working there," he told BBC Radio 4's Today.
"The debate has clearly become very, very fractious. As a businessman it is not my place to tell Scottish voters how to vote in next week's referendum.
"But I will say two things. From a business perspective there will be economic consequences to a Yes vote, not just in uncertainty but some of the turmoil we are hearing about.
"And it is also the case that it does cost more money to trade in parts of Scotland and therefore those hard costs, in the event of a Yes vote, are more likely to be passed on."
He went on: "On the day after the referendum the shops are going to open on time, nothing will change. For various reasons - regulation and transport costs etc - it does currently cost more money to serve parts of Scotland.
"Most retailers don't run different prices, they absorb that in the totality. If you go forward several years and you see a divergence of different things - particularly currency - that creates the likelihood, not the certainty, that costs would be higher.
"And when you are talking about two different countries it is most probable that most retailers would then start pricing differently. My view would be that the likelihood is that that would lead to some higher prices."
Asked about the potential impact on the business model of the employee-owned business which operates department stores and Waitrose supermarkets, he said: "Whatever happens in the referendum, we will continue and work extremely hard to make sure that we continue to be one partnership.
"But I would regret anything, obviously, which started to create divergence and really significant differences in the two markets that made it harder to achieve that."
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Scottish Finance Secretary John Swinney said other major retailers had rejected claims prices would rise.
"Charlie Mayfield is entitled to his opinion," he told Today. "But I noticed at the weekend that the line of argument being pursued by the Better Together campaign - which is in a letter that has gone to all households or many households in Scotland - suggesting this very point in connection with Tesco was rubbished by Tesco at the weekend.
"So I think the argument is one that is firmly contested by other retailers."
Pro-independence campaigners called for the withdrawal of the leaflets after a letter emerged from Tesco customer services which said there was "no truth" in the claim.
The company said the referendum is a "matter for the Scottish people" and that it has a neutral position on the debate.
The costs of supplying food in different markets can vary depending on labour and energy costs and government levies on some products, Tesco said, but added that suggesting a Yes vote would lead to an increase in food prices was "entirely speculative".
This comes as the head of the country's largest asset manager said that an independent Scotland would be a "big success".
Martin Gilbert, chief executive of Aberdeen Asset Management, told the Press and Journal newspaper: "Most sensible people now accept that Scotland would be prosperous with either outcome in the current constitutional debate.
"A sterling union would be both desirable and highly likely whatever is said in London now. Sterlingisation, that is keeping the pound come what may, would be a pretty good option.
"Low or no debt would be the position if an independent Scotland were denied access to Bank of England financial assets, and that would leave the newly-independent country in both budget and balance of payments surplus - not a bad start."