Carl Bildt suggested a "Yes" vote would lead to the "Balkanisation of the British Isles" and set off "unforeseen chain reactions".
Mr Salmond said the use of the word "Balkanisation" was insulting to the democratic process in Scotland.
But a spokesman for Mr Bildt said the politician stood by his comments.
The people of Scotland go to the polls on 18 September when they will be asked the "Yes/No" question: "Should Scotland be an independent country?"
Mr Salmond said the Swede's remarks, made in the Financial Times newspaper, were not only insulting to Scotland but to the Balkan countries that had joined the EU.
Both Croatia and Slovenia have become EU member states since the bloody wars that tore Yugoslavia apart in the 1990s.
Mr Bildt is a former prime minister of Sweden who also served as the UN's special envoy to the Balkans between 1999 and 2001.
The FT quoted him saying that Scottish independence would have "more profound implications than people think".
He added in the piece: "The Balkanisation of the British Isles is something we are not looking forward to. It opens up a lot, primarily in Scotland but also in the UK.
"What are the implications for the Irish question?" he asked. "What happens in Ulster?"
In a BBC interview, the Mr Salmond took exception to these remarks.
He said: "I think the term Balkanisation was very foolish.
"Insulting to this democratic process in Scotland but also insulting to the new European member states from the Balkans who are now part of the democracy of the European Union."
Slovenia has been in the EU for 10 years and Croatia became the newest member state last year.
Montenegro, Serbia and the former Yugoslav republic of Macedonia are all candidates for EU membership.
UK Prime Minister, David Cameron, was in Sweden for talks on the future of the EU with other centre-right leaders.
At a news conference with Mr Cameron, Swedish Prime Minister, Fredric Reinfeldt, chose not to echo his foreign minister's remarks.
He said: "We also have a lot of experiences in referendums throughout Europe and we have learned to respect the results and not to speculate in advance."
Sweden's shadow foreign minister, Urban Ahlin, said "unfortunately we have a foreign minister with a specialty in insulting other nations.
"I think he's insulting the people of Scotland by comparing a democratic referendum with 'Balkanisation'."
However, Mr Bildt is said to be standing by his remarks.
The Scottish Liberal Democrat leader, Willie Rennie, said the comments reflected wider international concern.
He explained: "Balkanisation is not a term that I would use but it's quite clear that leaders across the world are expressing concern about the United Kingdom because the UK is a force for good across the globe."
The SNP often draws inspiration from Scandinavian countries - including Sweden - for its vision of what an independent Scotland could achieve.
Mr Bildt is not the only international figure to have commented on Scotland's future in recent days.
Last Thursday, the US president Barack Obama said that America had a "great interest" in ensuring that the UK remained "united".
He also stressed that the decision on independence was for Scottish voters.
In his BBC interview, the first minister said the remarks were "low level" on the Richter scale of presidential interventions.
But he appeared to suggest that they could still be counter productive.
Mr Salmond said: "I'm not sure if President Obama is familiar with the Scottish word 'thrawn'.
"It means more than stubborn. It means people don't appreciate being told what to do, I think."
Mr Salmond said the president's comments had come as "a surprise" because the US had declared itself "neutral" in the referendum campaign.
He also noted that the US had previously acknowledged the democratic nature of the Scottish debate.
The vote on Scotland's future on September 18th was agreed between the UK and Scottish governments.
Scotland's First Minister Alex Salmond said comments by Sweden's foreign minister on Scottish independence were "very foolish".