In the Sinnoh-based games, the player can only use the Azure Flute once they have entered the Hall of Fame and obtained the National Pokédex. When the player reaches the Spear Pillar at the top of Mount Coronet and steps one tile north from the entrance, they will be prompted to use the flute, which will play a unique and eerie tune and reload the Spear Pillar map with a steep staircase that leads to the Hall of Origin. After it is used and once Arceus is caught, the Azure Flute will no longer trigger the entrance to the Hall of Origin when played at the Spear Pillar and the message "The Azure Flute echoed hollowly..." will appear. Should the player knock out Arceus, then the Azure Flute can be used to summon Arceus again.
The Azure Flute was never distributed in the Generation IV games.
Junichi Masuda revealed in an interview with Nintendo World Report in 2013 that the Azure Flute was thought to be too confusing for players to use, leading to the decision to not distribute it.[1]
Despite the Azure Flute never having been distributed, the Wonder Card text for the Arceus distributed during Pokémon's 20th Anniversary made reference to it.
In Pokémon Diamond, Pearl, and Platinum, simply possessing the Azure Flute (such as by modifying the save file to directly add the Azure Flute to the Bag) does not grant access to the Hall of Origin. The player must actually receive a Wonder Card with the Azure Flute through Mystery Gift and obtain the flute from the Poké Mart deliveryman, which sets the event flag necessary to use the flute.
In Pokémon Diamond, Pearl, and Platinum, the Azure Flute is the only event item that was never distributed, though the other event items were only distributed to Platinum.