Minister for Gender Equality and Work Life Paulina Brandberg has previously called her fear of bananas "the world's weirdest phobia".
The emails were published by the local newspaper Expressen and show the minister's office requested there were "no traces of bananas be in the room" due to a "strong allergy" when organising a meeting with a colleague.
Brandberg told Expressen that she was "getting professional help with" her phobia.
However, the Swedish Prime Minister Ul Kristersson hit back at the release of the emails and said her work as a government official had not been affected.
"I have all the respect for people who have different phobias," he said.
"I am disturbed when a hard-working cabinet minister is almost reduced to a phobia, and people make fun of it. I think you should be too good for that."
