Trade Minister Ann Linde led a business team last week and faced criticism for wearing a headscarf, or hijab.
Sweden says it has the world's first "feminist government".
A prominent Iranian women's rights activist and Swedish politicians have criticised the decision.
"It is ruinous to what is called a feminist foreign policy" said Liberal party chief Jan Bjorklund, who said Iran oppressed women through legislation.
The Swedish government should have requested that female members of the delegation should not have been required to wear a headscarf, he said, and that if the request were not granted any trade agreements should have been signed in Sweden or a third country.
But Ms Linde told the Aftonbladet newspaper that she was not willing to break Iranian law. She said that since the only other option would be to send an all-male delegation, she was required to wear a headscarf.
Swedish Prime Minister Stefan Lofven was also in Iran and said he raised human rights issues with Iranian President Hassan Rouhani.
Masih Alinejad, an Iranian journalist and activist, posted an image of Swedish Deputy Prime Minister Isabella Lovin signing a climate bill surrounded by female colleagues earlier this month next to one of several female Swedish government officials wearing headscarves and greeting Mr Rouhani.
The image of Ms Lovin was widely seen as mocking a picture of Donald Trump signing an anti-abortion executive order surrounded by male aides and advisers.
Women in the Swedish government "should have condemned an equally unfair situation in Iran," Ms Alinejad posted to My Stealthy Freedom, a popular Facebook page she runs that encourages Iranian women to post pictures of themselves without the hijab.
"Because if you are feminists and you care about equality then you should challenge inequality everywhere," she told the BBC. "They must stand for their own values."
The Swedish government says that "equality between women and men is a fundamental aim of Swedish foreign policy".
In 2015, several media reports noted that former US First Lady Michelle Obama did not wear a headscarf during a visit to Saudi Arabia after the death of King Abdullah, although numerous foreign female leaders and dignitaries had previously done so.
Foreign women are not required to wear a headscarf in the country, unlike in Iran.
Ms Linde said she would not wear one during an upcoming visit to Saudi Arabia.