The wildlife publication threatened to delete its profile entirely should the Facebook-owned firm claim the right to sell users' photographs without payment or notification.
"We are very concerned with the direction of the proposed new terms of service and if they remain as presented we may close our account," said National Geographic in a statement.
Instagram sparked a backlash this week when it announced it is claiming the right for businesses to "pay us to display your username, likeness, photos, in connection with paid or sponsored content or promotions, without any compensation to you".
However, company CEO Kevin Systrom has since downplayed reports that the firm planning to profit from users' photos, insisting that the revised licensing agreement was poorly worded.
"Since making these changes, we've heard loud and clear that many users are confused and upset about what the changes mean," he said.
Instagram is currently "working on updated language" for its new terms and conditions.