Within 24 hours, the ministry had taken the commercial off the air and asked Twitter and YouTube to remove it from their platforms.
In an email to Twitter, the ministry said the videos were "detrimental to the portrayal of women in the interest of decency and morality" and violated the digital media ethics code.
In a statement Monday, Layer'r Shot apologized for the television advertisements, saying that they "never intended to hurt anyone's sentiments or feelings or outrage any woman's modesty or promote any sort of culture, as wrongly perceived by some."
The brand said it had voluntarily asked all its media partners to stop broadcasting the advertisements from Saturday with immediate effect.
Even after the commercial was taken down, it continued to cause a controversy.
Actress Richa Chadha was among those registering her disgust, calling the makers of the commercial "filth."
"Creatives, script, agency, client, casting... does everyone think rape is a joke?," Chadha tweeted.
Responding to Chadha's Tweet, Quantico star Priyanka Chopra called the ad "shameful and disgusting" and said she was glad that the ministry has taken it down.
Film writer and director Farhan Khan also slammed the advertisement.
"What incredibly tasteless and twisted minds it must take to think up, approve and create these stinking body spray 'gang rape' innuendo ads. Shameful," tweeted Khan, who is also a United Nations Women's Goodwill Ambassador.
Actress Swara Bhasker said both the perfume brand and its marketing agency had been "tone deaf" given the alleged gang rape of the teenager in an upscale part of Hyderabad last Saturday.
The case has shocked the state of Telangana, of which Hyderabad is the capital. Telangana's home minister Mohammed Mahmood Ali said on Saturday that "strong action will be taken against all the offenders, irrespective of their background."
It was "a ghastly incident," the minister tweeted on Saturday.
Source : CNN, Additional reporting by CNN's Esha Mitra