Otiko Djaba told girls at a senior school in eastern Ghana they should demand respect and equality but added short dresses "can attract someone who would want to rape or defile you.
"You must be responsible for the choices you make," she said during a visit last week.
The minister's comments have been widely criticised, with many arguing they wrongly place the blame for rape and sexual assault on the victim rather than the perpetrator.
Djaba joins a growing list of political figures around the world who have caused outrage by making a direct link between what a woman wears and rape.
Clothing for girls and women is a mix of Western imports and traditional print fabrics that are used for tailor-made outfits.
Above-the-knee dresses and skirts are not uncommon, particularly in cities such as the capital, Accra.
But feminist and sex educationalist Nana Akosua Hanson said women who wear short skirts still attract unwanted attention.
On the street, many women said the fear of being judged and leered at, as well as advice from church, stopped them from wearing less, even in temperatures that rarely dip below 30 degrees Celsius (86 degrees Fahrenheit).
The teenager said her church also preached against "provocative" clothing. "It makes the one who gets attracted to you to sin," she told AFP.
Boatemaa Akua Benedicte, a 24-year-old nursing graduate wearing a flared dress with an African print headband, said a woman was responsible if she was attacked while wearing a short skirt.
The rapist should shoulder only some of the blame, she added.
High school student Maria Abdullha, 17, also shied away from short dresses. "If you wear short clothing, people will think bad about you," she said.
But she said the outcry, particularly on social media, indicated there had been a "serious rise in consciousness" about the issue of rape and sexual assault.
Hanson runs sex education workshops for young people in Accra, focusing on consent and tackling rape culture.
She said the minister had at least opened up a public debate about the issue.
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