Efficiency is analogous to corruption in Civilization games. The further away a base is from your Headquarters, the higher the proportion of energy is lost due to inefficiency. Minerals and nutrients are not affected. If you have a large number of bases, you will also receive more drones at bases due to "bureaucracy". The less efficient the base, the more drones will appear. Efficiency is modified by the map size. On larger maps, the rate at which efficiency drops due to distance from your Headquarters decreases, and the number of bases required to increase bureaucracy drones increases.
You have an Efficiency rating based on your policies in Social Engineering. Certain policies, such as Planned economics, decrease your overall efficiency, and others such as Democratic will increase it. A negative efficiency rating can wreck the energy production of a large empire as well as exasperate drones.
A Children's Creche, among other benefits, increases the efficiency rating of its base slightly. This makes it one of the most important facilities.
Consider relocating your Headquarters to a central position in order to increase efficiency.
The Hive is immune to inefficiency. This means if the efficiency rating is negative, it is treated as 0, allowing the Hive to run both Police State and Planned simultaneously without penalty - although any efficiency bonuses such as from Knowledge will be simply absorbed.
The number of cities and the size of map will have an effect on Efficiency. There is a threshold, and once you past that, the actual loss of energy and increase of drone will appear. Huge Planet: 11 Bases. Large : 9. Standard : 6 . Small : 5 . Tiny : 3 Bases.