Devon Docherty, Scottish campaigns manager at Protect the Wild, said refusing a licence was a “victory for compassion, for science and for common sense”.
She added: “Thousands of young seabirds have been spared from a brutal death because NatureScot chose to follow the evidence rather than simply rubber-stamp another licence to kill.”
Scottish animal campaigns charity, OneKind, also welcomed the decision.
Chief executive Jason Rose said: “We are very relieved that the lives thousands of young gannets will be spared this year, and many more birds won’t bear the emotional toll of disruption to their lives, families and communities.”
The Scottish Seabird Centre, said it was the “right decision” for Scotland’s seabirds.
Emily Burton, conservation manager, said: “Gannet populations have suffered significant declines, and many colonies are still recovering from the impacts of avian influenza.”
More than 106,000 people signed a petition, external calling for the Scottish government to prohibit the hunt.
The cultural significance of the hunt is recognised under the Wildlife and Countryside Act 1981, and modern hunts require a licence from NatureScot.