The best source of bodies will depend on their required number. If you are sticking with 3 days usage limit and necessity of a physical contact to reanimate them you might have enough bodies without implementation of any special system except body collection. So, let's examine possible sources.
1. Bodies of country residents died of natural (or not so natural) causes
Your own citizens die every day. Some of them are just old, some are sick, and some were victims of a bar brawl gone wrong. Instead of burning, burying, or any other disposal procedure, all those bodies must be submitted to a special temple, government office, etc. It can be a great honour for a family if a body of their deceased was used for a magic ritual.
This will work very well if the ruler is perceived as a deity. "Serve your God in life and after it, as well!" If approached correctly, the government may even get some money as families will pay for the bodies to be used.
Country residents will provide a steady supply of bodies. It might be not enough for an army, but it should be fine for small magic applications. Tropical climates would result in faster degradation of flesh. Cold climates would preserve them longer and fresher.
2. Bodies of fallen soldiers
If your country constantly wages wars, you can collect bodies from battlefields and put them to good use. That would be an ideal source for a battle mage.
You need to consider that as soon as your enemies realise what's going on, they will start to destroy bodies. Something like Greek fire would be an effective way to prevent mages from getting anything useful. The downside is that the land will be damaged in the process (probably, not to the point that it cannot recover).
3. Slaves (warriors and citizens of the lost side)
As Josh King mentioned it can be a good source of bodies. There is a problem here, though. Wars are very expensive. It is also not very practical for a conqueror to kill or enslave the entire population of a conquered country. Land with no people to work it does not bring prosperity, it is a liability (too hard to protect).
So, you'll have to settle for PoW and some kind of tribute paid in humans. Unfortunately, this also poses a problem. PoW are mostly warriors, so you'll have to deal with higher security requirements, frequent revolts, jailbreaks, etc. Too much pain, if you ask me. Slaves that come as a part of tributes might be more timid and complacent, but they also know freedom and will not be very happy to be sacrificed. So, again, security problems...
4. Sacrificial, home-bred slaves*
If you are interested mainly in bodies, breeding slaves is a much more effective solution than enslaving other peoples. Here and now you can add fresh blood, of course, but the main population of slaves should be very low intelligence with high fertility rates. Think human rabbits.
No revolts, no uprisings, no war expenses, and as many slaves as you need just on the next corner. Moreover, you'll have a wide choice of bodies to pick from. Your government will be very pleased.
5. Other options
You may also choose to have sacrificial castes, third children of third children, pilgrims, sick and deformed people, etc. It really depends on how much you want to 1) explore moral and ethical norms, and 2) get things done.
*This idea might sound very wrong to a modern person, but in your world, the ideas of humanism haven't spread, so no need to worry about an ethic side of this.