I bred hamsters when I was a kid and they eat their young as well. The reasons were due to any foreign scent on the litter. You cannot touch them. If they smell anything on them they will eat them. Seperate the father and leave just the mother to feed the litter.
As soon as they open their eyes and can eat on their own I would get the mother out of there also.

This may help solve your problem if rats are the same as hamsters. I'm sure it will help as they are all rodents with similar habits.