The Planetary Protection Shield was created by the Chozo on Zebes to protect them from attack. It is known that they bolstered their defenses from the first Space Pirate attack, and this may be one of the results of that. However, the second Pirate assault on Zebes (which won them the planet) broke through the shield. The Space Pirate Flagship used the gravitational field of a micro black hole to ultimately break the shield.
Mother Brain later remarks that her own "shield is made by molecule transference of Zebetite. It uses the same system that governs the planet's shield." In Metroid Prime 3: Corruption, a similar technology, the defense system generator is also disabled, although the roles are reversed as Samus Aran disables the generator, which is protecting the Pirate Homeworld.