On Tuesday, a journalist for Sveriges Radio (SR) asked ambassador Isaac Bachman on air: "Are Jews themselves responsible for the progression of anti-Semitism?"
The ambassador appeared shocked by the suggestion, and replied: "I purely and simply reject the question."
When the journalist asked "Why?", Bachman said: "There was no reason to ask this question."
The station removed the programme from its online archive and issued a full apology.
"We offer our fullest apologies for this question. It was misleading and put blame on individuals and on a vilified group," SR's senior management said in a statement on its website.
"The Jewish community has suffered a horrible act of terror and has all our sympathy," the statement added.
Relations between Israel and Sweden are already strained following the Swedish parliament's decision last year to formally recognise the Palestinian state. Israel initially recalled its ambassador for a month in protest.
Last week Isaac Bachman told The Local: “The recognition of Palestine, including the additional Swedish steps and policies vis-a-vis the Palestinians has not created a better atmosphere between Israel and Sweden.”
“We were not consulted on this matter, and it is obvious that the recognition came just a few weeks after the end of a bloody rain of fire on Israel from Gaza.”
But Sweden has stood by its decision and last week announced a $1.5 billion Palestinian aid package.
"According to us Palestine is now a state. Our expectations of Palestine and their leadership will therefore increase," Prime Minister Stefan Löfven told reporters during a visit to Stockholm by the Palestinian President Mahmoud Abbas.
In the wake of the Copenhagen shooting at a synagogue, following an earlier attack on a cultural event attended by Swedish artist Lars Vilks, many Jews say they are frightened about violence spreading over the border.