Katarina Bergehed, responsible for women's issues in Amnesty International Sweden, laments the decision.
"Amnesty Sweden voted against the proposal. Above all, we're not that certain that the organization has proved well enough that only the decriminalization of all activities surrounding sex trade would improve the situation regarding the rights of people selling sex," Bergehed tells Swedish Radio News.
However, a majority of the 400 participants from 70 countries who took part in the meeting believe that decriminalizing prostitution would benefit the weakest and most exposed groups, like sex workers.
Bergehed explains how this majority of Amnesty members see the issue.
"As long as the competent authorities focus on fighting certain parts of prostitution which are illegal, this will affect people who sell sex, which will also indirectly be criminalized," she says.
The decision was controversial even before it was officially made, with several women's rights organizations, doctors and celebrities including Meryl Streep and Kate Winslet warning that it could harm the NGO's reputation.
Between 200-300 people have since revoked their memberships with the Swedish branch of the organization in protest, according to news agency TT.