A "Yes" vote on September 18 would spark a painful process raising questions about relationships with Ireland and the UK's role in European politics, Carl Bildt said.
As well as raising his concern about the Scottish referendum, he warned that taking the UK out of the EU would be a "disaster".
Prime Minister David Cameron proposes holding a referendum on the UK's membership by 2017.
He predicts unforeseen chain reactions if Scots first vote to leave the rest of the UK.
"The Balkanisation of the British Isles is something we are not looking forward to," he told the FT.
"It opens up a lot, primarily in Scotland but also in the UK. What are the implications for the Irish question? What happens in Ulster?"
The UK may lose votes in EU decision-making, he claimed.
Losing the UK after a second referendum would be a significant setback.
"The EU would lose a significant element of global clout. It would be an even bigger disaster for the UK," he added.
A spokesman for pro-independence campaign group Yes Scotland said: "The Nordic states set a fine example of how neighbouring countries can cooperate and share a social union without a political one. A Yes vote in September provides the UK with an opportunity to emulate that.
"Scotland has been a member of the European Union for more than 40 years and we can look forward to our continued membership with independence. The only foreseeable future disruption to the EU from these islands comes from Westminster's proposed in/out referendum."
A Scottish Government spokesman said: "These comments do not reflect the reality of Scotland's referendum process, which is a model of democracy and of how such processes should be conducted, and which has been cited as such internationally, including by the US Secretary of State.
"An independent Scotland will play our full part in the international community, bringing a peaceful, progressive and constructive voice to global affairs."