As far as I can find in the rules, negative levels are always described in conjunction with energy drain, and are even listed together as one special ability in some cases. Usually there will be a line like the following:
Each successful energy drain attack bestows one or more negative
levels
Followed by a description of the effects of a negative level. As far as I can tell, this is all we have to go on for what negative levels are or where they come from. In other places in the rules, negative levels are often treated as synonymous with energy drain, or at least connected to it.
But what about abilities and effects that inflict negative levels but do not use terms like energy drain? What about an unholy weapon in the hands of a good creature? What about Fission?
Essentially, are negative levels actually synonymous with energy drain, or are they a more generic mechanic that is simply most often used to reflect the effects of energy drain attacks? Is a creature that is immune to energy drain immune to negative levels as a whole?
Best Answer
Negative Levels are a Direct Result of Energy Drain; but not Synonymous.
Enervation vs. Energy Drain
Enervation's Negative Levels don't last long enough for permanent level drain.
Energy Drain's negative levels do last long enough for permanent level drain, and also bestows a lot more per spell cast (metamagic aside); allowing that many more chances of failure to remove negative levels.
Unholy Weapon
Unholy weapons are imbued with the essence of evil [arguable connected to necromantic] energy and "curse" those that wield it, bestowing a negative level as long as it is wielded, but since it is not a permanent effect, it isn't drained.
Fission
This is, essentially, a temporary Clone. Your clone, in this case, is exactly like you, but "treated" as if you had two negative levels.
So in this instance, your clone will have double the following:
Now, if your clone dies before you rejoin, you are essentially losing a part of your life force. Necromancy has been described as the essence of life and death, so a part of your essence has just died off, and you would gain a negative level.
Now, if you die and your essence lives, then a bigger part of your life force has just died off, so you would now be your clone, with the two negative levels.
Has it been effectively drained? Arguably, yes, you drain a part of your essence so that part of your essence can have a life of its own. Although the psychic power of Fissure doesn't mention necromancy, in the power description, it can be inferred by the language used.
Context of reality could be like this; your energy gets drained whenever you donate blood (Energy Drain). The nurse literally drains your blood and puts that into a container. That blood, genetically, is you, just a smaller part of your entire blood supply (Fissure). If that blood supply isn't put back into you, you feel drained for probably a day (negative level) until your body naturally replenishes itself (removes its negative level). If that blood supply is put back into you, you feel rejuvenated immediately (negative level is gone).
Creature Immunity
We can look at Undead for example, of creatures that are immune to Energy Drain.
Undead, have no life force. Therefore, there is literally no "energy" to drain. What energy is being drained? One could infer Positive Energy. Undead are the result of reanimation from Negative Energy effects. Negative Levels don't count towards them, because they are made of that Energy.
Also, constructs are devoid of a life force. They are immune to necromantic effects.
Energy drain is a necromantic effect.
What would happen if a lawful good vampire picks up an Unholy Weapon? That would be a good question in and of itself. Since the Unholy Weapon, technically isn't draining the vampire, I would say both effects happen. He gains a negative level, but is also healed. That would have to be a judgement call by the DM.
Some creatures, such as Hellbred, can use Unholy Weapons, even though they are good aligned. Once again, since it is more of a curse, they aren't being drained, they can pick that bad boy up and swing it around for the cause of good.
Conclusion
Negative Levels, although the result of Energy Drain, are not necessarily Energy Drain in and of itself. Some other times, it can be simply a curse or a consequence of doing/having something that you are not supposed to.
Your DM would have to decide if Negative Level consequences count as necromantic effects. It would make sense, not break anyone's game, and allow that lawful good vampire to wield weapons that Hellbred can.