The star took down an Instagram post of the cover, saying: “I don’t want to be hypocritical or hurt anyone.”
The daughter of the late Michael Jackson confirmed to her fans last month she is bisexual.
The 20-year-old’s appearance on the September issue of Harper’s Bazaar in Singapore saw her labelled “hypocritical” in an op-ed by Gay Star News’ entertainment editor.
In the piece, Jamie Tabberer points out that gay sex in Singapore is still illegal and punishable by up to two years in prison.
He also took issue with the fact Jackson appeared not to address this when speaking to the magazine.
“As a member of the [LGBT] community, her decision is all the more disappointing,” Tabberer wrote.
“On the one hand, I consider her possible immaturity… On the other, I respect her enough to hold her accountable for her decisions.
“She may be a very young woman with a lot to learn, but she’s also, definitely, an adult.”
The Gay Star News tweeted Jackson with a link to the article saying: “C’mon Paris Jackson.”
Paris replied saying she had been “grateful” for the opportunity to appear on the cover but that she had not known about the gay rights in the country, and as a consequence would delete her post.
She added that her support for her “fellow LGBTQ+ community comes first before my love for fashion.”
In follow up tweets, however, Jackson defended her decision to appear on the cover, saying it should be “celebrated” as a step forwards in a country with such conservative views.
She also said that the cover was not just intended for Singapore but for “several” different countries.
Hearst, which publishes Harper’s Bazaar, confirmed to the BBC that Jackson would be appearing on September covers for seven other countries, including Brazil, Poland and Spain.
As part of the shoot Jackson did not give a full interview, but instead gave the magazine a quote about what family meant to her.
“I have a family that I’m related to by blood and family that I’m not,” she is quoted as saying.
“Family to me is a feeling of tribe – people in your life who you are connected to on the deepest of levels, who make you feel safe and at home no matter where you are in the world.
“They tell you ‘no’ when you need to hear it, and they love you unconditionally for your soul, nothing less than that. Family is a feeling.”
Jackson’s fans were quick to defend her on Twitter, with Wilson Philips singer Carnie Wilson among those to tweet in support.
Gay rights in Singapore remains a fraught issue and recent years have seen courts upholding a law criminalising sex between adult men.
In the past, though, the government has said it would “not take a proactive approach” towards enforcing the relevant legislation.
Jackson opened up about her sexuality during an Instagram Q&A last month after a fan asked if she was bisexual.
“That’s what you guys call it so I guess, but who needs labels?” she replied.
Following coverage of the story, she later elaborated she had been out since she was 14, commenting on Twitter that she didn’t understand why it was newsworthy.
“I’ve been apart [sic] of the community for years,” she wrote. “This is not news.”