Margot Wallström said on Monday that Saudi officials had stopped her from making her opening address to the meeting due to her stance on human rights.
But Arab foreign ministers later criticised Sweden for its comments about Saudi Arabia.
“The ministers have voiced their condemnation and astonishment at the issuance of such statements that are incompatible with the fact that the Constitution of the Kingdom of Saudi Arabia is based on Sharia,” read a statement issued by the ministers following their Arab League meeting in Cairo and reported by the Swedish media on Tuesday.
“Sharia has guaranteed human rights and preserved people’s lives, possessions, honour and dignity. The ministers consider the comments as irresponsible and unacceptable,” the statement added.
Wallström had been invited as an honorary guest to the Arab ministers' meeting in praise of her government's decision to recognise Palestine in October.
Her cancelled opening speech – published by the Swedish foreign ministry – mentioned neither Saudi Arabia nor Wallström's feminist foreign policy agenda but stressed women's and human rights.
Wallström's press secretary Erik Boman told The Local on Tuesday that the Arab League's statement "should be interpreted as a way of Saudi Arabia trying to save its face".
"The statement was made public yesterday, and we knew about it," he said.
"It is one of very many statements on different issues released by the Arab League after a meeting – by tradition they do that kind of thing."
Earlier in the day, Sweden's Prime Minister said it was right to question Saudi Arabia’s human rights abuses.
“Margot Wallström was invited as a guest of honour. Of course it’s a pity it was cancelled but when we see something wrong, like human rights violations, we have to express what we think,” he told Swedish public broadcaster SVT.
Margot Wallström on a visit to Finland. Photo: TT
On Monday Wallström said it was a "shame" that she had been blocked from speaking.
"The explanation we have been given is that Sweden has highlighted the situation for democracy and human rights and that is why they do not want me to speak," she told Swedish news agency TT.
An Arab diplomat confirmed to the AFP news agency that Saudi Arabia had stopped the Swede from making her opening speech.
Meanwhile the EU has expressed concerns over the move.
"We regret that the Swedish foreign minister was not able to deliver her speech," European Commission spokeswoman Maja Kocijancic told a press briefing on Tuesday.
EU foreign affairs chief Federica Mogherini will speak to Wallström and Arab League chief Nabil al-Arabi "to understand this situation", she added.
But the Social Democrat party – of which Margot Wallström is a member – has indicated that it would like to preserve the agreement in some form, although the issue has caused an internal party rift.