Romson sparked debate after she spoke on public broadcaster SVT's breakfast show 'Gomorron Sverige' on Tuesday morning, while discussing housing minister Mehmet Kaplan's resignation.
She praised her Green Party colleague's efforts working with Muslim youth associations in Sweden, including his former role leading the non-politically affiliated group Sweden's Young Muslims.
"He has been chairman of Young Muslims in tough situations like the September 11th accidents," she said.
Her words were quickly criticized by viewers, who pointed out that nearly 3,000 people died in the al-Qaida led 2001 attacks on New York's World Trade Center, Washington's Pentagon building and United Airlines Flight 93.
"Did Romson just call 9/11 'the September 11th accidents' on SVT?? In that case, talk about reducing [the significance] of one of the world's biggest terror attacks," wrote defence expert Johanne Hildebrandt on Twitter.
Kallade Romson precis 9/11 för "elfte septemberolyckorna" på SVT?? I så fall, snacka om att förminska en av världens största terrorattacker- Johanne Hildebrandt (@JohanneH) April 19, 2016
"Had to listen again. And yes, Sweden's Deputy Prime Minister Åsa Romson talked about the 'September 11th accident'," tweeted Johan Ingerö of Swedish liberal think-tank Timbro.
Blev tvungen att lyssna igen. Och jo, Sveriges vice statsminister Åsa Romson talade om "elfte september-olyckan".- Johan Ingerö (@JohanIngero) April 19, 2016
However, others defended her, saying she had misspoken and that the focus should instead be on issues.
Ohhh. Now I get it. Cut the poor lady some slack. I'm American and I'm not offended. https://t.co/YsNhPmpDiW- Christopher Banks (@cmbsweden) April 19, 2016
The environment minister, who is scheduled to attend a UN climate meeting in New York on Wednesday and Thursday, later clarified her comments in an email sent to The Local.
"Let there be no doubt: the attacks on the World Trade Center in New York City on September 11th 2001 were one of the most vile acts of terror and disastrous violations of the open, free and democratic society in modern history," she said.
"The tragedy for the world and the families of the almost 3,000 human beings who perished as a result of the attack cannot be overstated."
She also told Swedish newspaper Aftonbladet that she had been making a point about the harsh debate on integration that followed, suggesting that she had meant to describe it as a misfortune rather than an accident.
"We refuse to let terror set the agenda. Not then, not now. We must not let extremism cloud our judgement or fall to the low point where immigrants or muslims are collectively blamed as a result of the acts of extremists," she added to The Local.
Her comments came just a day after US presidential hopeful Donald Trump referred to the attacks as '7-Eleven', getting the figures confused with the name of a major convenience store chain, so Romson was not alone in her woes.
However, it is not the first time Swedish minister has grabbed headlines over ill-advised comments.
Last year she was at the centre of controversy after she twice made ill-advised comments about the Nazi concentration camp Auschwitz and after it was revealed she had used toxic paint on her houseboat.
Romson sparked a huge wave of criticism at the time when she described the migrant crisis in Europe as "the new Auschwitz" in a live television debate. She was later forced to apologize after commentators accused her of disrespecting the victims of the Holocaust.
She then found herself on the receiving end of social media humour after she inaccurately placed the Nazi concentration camp "in southern Germany" rather than Poland.
Her latest gaffe comes at an inopportune time for the Swedish Greens, who on Tuesday were still battling the aftermath of Mehmet Kaplan's resignation as well as Vattenfall's brown coal sales.