Dundee-based pensions and savings firm Alliance Trust has started registering companies in England after warning of "uncertainty" over the Scottish independence referendum.

The FTSE 250 firm is the latest bluechip name in Scotland's financial establishment to warn that independence poses a risk for its business. Last week Standard Life said it could quit Scotland if it became an independent country. Royal Bank of Scotland has said a yes vote would damage its credit rating, while Lloyds Banking Group added this week that a yes vote would have a "material impact" on the business. The boss of insurance giant Aviva, however, told Sky News that independence was not an issue for his company.

Alliance Trust, established in 1888 in Dundee, described the referendum as significant.

Katherine Garrett-Cox, chief executive of Alliance Trust, said the company had started to create companies registered in England, as part of its "duty" to customers.

But it was "premature" to talk about moving Alliance Trust's headquarters out of Dundee, she said. "We have every intention of making sure we are there for a long time, but this is about creating optionality because we still don't know the answers to some pretty important questions."

Around 80% of Alliance's customers and two thirds of its shareholders are outside Scotland. The firm has an office in London, but 230 of its 260 staff are in Scotland. "So [the referendum] is a significant issue for us and we want to be absolutely clear and transparent to our customers and shareholders," Garrett-Cox said. "What our customers are telling us is that [they want to ensure] the tax wrap status of their pensions and savings is protected regardless of political outcomes, so that is why we are seeking to reassure them, that we have got it covered. One of the risks we have outlined in our report today ... is that we don't know how taxation and jurisdiction issues will be applicable in an independent Scotland."

The company's announcement coincided with a speech from the chief secretary to the Treasury, Danny Alexander, who warned that Scottish householders would pay more for pensions under independence because they will lose the insurance guarantee of the UK Pension Protection Fund.

The Scottish National Party has said it will create its own protection fund, but Alexander argued this will drive up costs because firms would be less able to spread risk.

He also reiterated the government's opposition to the SNP's preferred option of letting Scotland join a currency union, likening it to "embarking on a damaging divorce, and insisting we should still share a credit card". Speaking to the National Association of Pension Funds, he said: "I've seen some people suggest we are not serious about refusing a currency union. Let's call this the John McEnroe defence. Except in this instance it's not just one person they're shouting at, but three. And our decision – taken in the best interests of Scotland and the rest of the UK – is final."

Kenneth Gibson, a Scottish Nationalist member of the Scottish parliament, who chairs the finance committee, said: "People across Scotland are growing tired of Westminster's attempts to bully and scaremonger on independence." Gibson also highlighted Aviva's position, describing it as "the latest company to say that independence is not an issue for them". A spokesperson for the the Better Off Together campaign seized on Alliance's announcement: "With each passing day the reality of the risks involved with leaving the UK become clearer."

As well as pillars of the Scottish financial establishment, Shell and BP have led the warnings from the North Sea oil and gas sector over the consequences of a go-it-alone vote.

With the yes campaign lagging in the polls, analysts at Citi group said a positive vote looked unlikely. However in a report published on Friday, Citi drew attention to three risks that would face an independent Scotland: a deficit well above UK levels, the fiscal hazard of being on the hook for a banking sector 1,000 greater than the economy, as well as currency and monetary uncertainty. "Referendum risk" was on the rise across Europe, the analysts said, although they concluded that a possible vote on Britain's continued EU membership in 2017 was the most underappreciated. "Even a failed vote might set the stage for market-moving surprise and generate heightened uncertainty".