The Swedish government denied any links between the replacement of Per Thöresson and the planned sale of 22 Gripen aircraft -- approved by the Swiss parliament last year, but still pending a May 18 referendum on financing.
"Everyone working at the (Swedish) foreign ministry is part of a rotation system," foreign ministry spokeswoman Catalina Axelsson told AFP.
"This is a rotation that has been planned since last year."
In February Swedish public radio revealed plans by Sweden's embassy in Bern to influence the outcome of the referendum, with financial backing from the Gripen maker Saab.
The news sparked outrage among groups opposed to the deal in Switzerland, that criticised what they saw as outside interference, and led to Saab withdrawing its finances from the campaign.
The Gripen sale is worth 23 billion kronor (€2.5 billion, $3.5 billion) and is important to Sweden which has sought other buyers to help finance its own purchase of 60 jets.
According to classified documents cited by SR on Tuesday revealing further details of Swedish lobbying, Thöresson tracked the opinions of Swiss parliamentarians and arranged private meetings to win over sceptics.
Swedish Foreign Minister Carl Bildt told SR that the embassy in Bern was just doing its job.
"Swedish ambassadors should support Swedish export efforts -- that's what they do and that's what they should do," Bildt said.
"It is part of their basic activities."
Sweden's foreign ministry announced in a statement last Thursday that Thöresson will become deputy chief of the Swedish permanent mission to the UN in New York.
The new ambassador to Switzerland, Magnus Holm, who previously held positions in Estonia, Germany and Japan, will take over the position next autumn.
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