One of the easiest ways of cloning Master Balls is to use the Battle Tower cloning glitch in the Pokémon Emerald game version. The items cloned in Pokémon Emerald, which is from the third generation Pokémon games, may also be traded in later Pokémon game versions.
Any items held by the Pokémon during the cloning process in the Battle Tower, such as the Master Ball, will also be cloned. The player gains access to the Battle Tower once he has beaten the Elite Four.
The following shows how to clone items in Pokémon Emerald:
After entering the Battle Tower, head to the PC on the far right and deposit any Pokémon.
Make the Pokémon hold the Master Ball, turn off the PC and then save the game.
Turn on the PC again and withdraw the Pokémon with the Master Ball. Walk over to the woman and enter any two Pokémon for battle.
When asked if it is OK to save the game, choose "Yes." Once the woman asks to save the game, reset the Game Boy Advance.
After the game resets, the Pokémon with the Master Ball will be back in the PC and also in the player's game bag.