Why did Israel need cities of refuge and how did they work?

The six cities of refuge.

As early as Deuteronomy, God gives some instructions for handling refugees of manslaughter. When a person killed another by accident, then the person who committed the act could flee to these refugee cities to seek asylum, where the elders of that city could hear the story as told by the refugee and determine a place for the refugee until a trial could be held. Why was such a system of entire cities necessary at the time, and how exactly might they have worked?

The Bible itself is pretty clear about the rules regarding someone seeking the safety of one of these cities. If a person must flee because they have committed manslaughter, that person must arrive at the gate of the refugee city and tell his story to the elders. The elders must then provide a place for the refugee and, if someone comes seeking revenge for the accidental death, provide protection from that person until the refugee can stand trial for the killing. Joshua includes a passage that they must provide protection until the death of the high priest of the time, and it's thought that the death of the high priest was so alarming to the Israelites that most dropped all desire for revenge. After the refugee stands trial and a verdict is rendered he may either return to his home, if he feels it is safe, or return to the city under protection and guard.

In ancient times, and still in modern superstitions, the gods were inviolable and their places of worship considered to be also places of safety. To do harm to or kill someone in these places was a sin beyond recompense. The size of the sanctuary often relied on the deity and culture, but these traditions extended to many ancient religions, and often to drag someone from the place in order to kill them was even worse than doing it on the spot.

Syrian Zaatari refugee camp, a modern refugee city.

Over time people began to take advantage of these social rules, and sanctuaries tended to draw crime in most cultures. This led to asylum rights to be restricted more and more to specific areas when crime became too much of a problem. For example, in Athens asylum rights were restricted to only the temple of Theseus. So, by the time of the Israelite's conquest and partitioning of the land, it had already been customary for sanctuaries to be specific places designated by law rather than general locations in places of worship.

Levite priests.

Since the Levites were mediators with God, it was thought that they would be the best judges to handle accidental killings, and perhaps their inclusion in the process would quell any notions of blind revenge from the victim's surviving friends and family.