On Facebook many branded the story "disgraceful" and said it lacked respect for the dead.
One user said: "Samoa Observer - you stupid, insensitive a*******. You showed that you don't care about LGBTQ as the photo you published on the front page and the pronoun you used for her just reinforces the abuse, insensitively [sic] and hate our brothers and sisters who identify as LGBT go through."
Another said: "Was it necessary to put that picture of [Jeanine] Tuivaki on the front page of the paper?. Yes she is a transgender person, but where is the respect for the dead ?. I am disgusted at the lack of Respect for this human being."
Louise Bartley-Devoe said: "Absolutely disgusting & disrespectful Samoa Observer!"; while Isaac Toafa said the coverage of Ms Tuivaiki's death was "a disgrace".
One blogger said it "disregards the rights of the victim, families and friends".
Journalism professor Mark Hayes reportedly described the article as "utterly disgraceful, inexcusable, [and] totally unprofessional".
"Media ethics classes will study this outrage for years to come as it's an awful example of how to absolutely not report these kinds of stories," he said.
A number of people on social media said they would write to complain about the story, while others suggested Ms Tuivaiki's family should sue the paper.
"Insensitive & disrespectful are understatements. This family should take legal action against SO!"
According to the Sunday Samoan, Ms Tuivaiki was found in the hall of the Catholic Church of Taufusi in the early hours of Friday morning local time.
Members of the church declined to comment to the paper, saying only that the matter had been referred to police.
A friend told the newspaper the circumstances surrounding her death were not yet clear, but she believed that if someone had found Ms Tuivaiki earlier she might have been saved.
The friend described Ms Tuivaiki as "someone who was very committed to the church and especially our youth".
"We are all shocked about what happened," the friend said.
"[She] was a loving person, very talented and [she] seemed very happy every day."
The Sunday Samoan has issued an apology to its readers, which will feature on the front page of tomorrow's Samoa Observer.
Penned by editor in chief Gatoaitele Savea Sano Malifa, and sent to the Herald, it said the photograph was placed alongside two stories about divisions in Samoa's religious communities as it appeared to have symbolic meaning. Religious division had caused violence, "painful disunity", and suffering, he said.
"That was how it felt when that photograph showed up. It was a sad sight.
"But then behind the sadness and the pain was the image of Jesus Christ.
"It was as if Jeanine Tuivaiki was telling Prime Minister Tuilaepa,Pope Francis, and Rev. Mauga Motu, to make friends with everyone, and let there be peace.
"That was the inspiration that guided us to put that photo on the paper's front page. It was never to demean, vilify or denigrate."
The photograph had been circulating on Facebook for a week, he said.
Mr Savea Sano Malifa ended by saying: "And so if you're offended by it still, all we can do is apologise."
Where to get help:
• Lifeline: 0800 543 354 (available 24/7)
• Suicide Crisis Helpline: 0508 828 865 (0508 TAUTOKO) (available 24/7)
• Youthline: 0800 376 633
• Kidsline: 0800 543 754 (available 24/7)
• Whatsup: 0800 942 8787 (1pm to 11pm)
• Depression helpline: 0800 111 757 (available 24/7)
If it is an emergency and you feel like you or someone else is at risk, call 111.
