The Naboo pilots found the droid control ship's shields to be too strong for their attacks to be effective within the time available for their mission. We can assume that this refers to the ray shielding, which could effectively dissipate blaster fire from the fighters within a distance short enough that the hull remains unharmed. The ship must have had powerful deflector shielding as well, in order to give it immunity to any physical attacks, such as figher collisions and the impact of any proton torpedoes fired by the Naboo.

There were two noteworthy incidents involving the Federation vessel's shield capabilities. The first was when three N-1 fighters flying and firing in formation managed to destroy a large antenna dish and were engulfed in the ensuing explosion. This demonstrates some kind of weakness; perhaps the shielding is less effective around structures with sharp edges, or perhaps the shielding is weaker in the presence of the dish transmissions. In any case, this incident demonstrates that the Naboo mission was not totally hopeless, although they may have needed to much more time before they could hope to eliminate the rest of the transcievers.

The second interesting incident was when Anakin Skywalker's violently spinning fighter penetrated the droid control ship by passing through the aperature of the starboard hold. The ineffectiveness of the shield at that moment needs explanation. Some commentators assume that deflector shields are only scalar phenomena, failing to differentiate between incoming and outgoing objects, which would mean that the shields would have to be lowered during the launch of Federation fighters. This would expose the ship's interior in a wide variety of combat situations, and is therefore unvelievably impractical. If we indulge this theory, for the sake of argument, then Skwyalker must have entered the hold while Federation craft were entering or exiting. More realistically, the shields may be directional, but they were temporarily turned inwards because of incoming Federation fighters. Skywalker's pursuers might have triggered this effect automatically.

Alternatively, there may have been something about Skwyalker's motion that allowed him to pass the shield unscathed. Conventionally, deflector shields are less effective on slow-moving objects; so perhaps the damaged N-1 fighter was moving slowly enough that it wasn't discriminated. However the N-1 seemed fast enough to be a dangerous projectile, even though it was slower than a proton torpedo, and therefore a well-designed deflector shield ought to have impeded or blocked it. Perhaps the permission of Anakin's N-1 had something to do with its spin; it looked as if the fighter had more rotational kinetic energy than linear kinetic energy. If deflector shields exert a complicated vector or tensor force then perhaps a transient configuration of the hangar shield had an effect that was concentrated against the fighter's spin, or which coupled the spin to the forward motion in some way.