Goren and Lauter studied genus 2 curves whose Jacobians are absolutely  simple and have complex multiplication (CM) by the ring of integers of a  quartic CM-field, and showed that if such a curve has bad reduction to  characteristic p then there is a solution to a certain  embedding problem.  An analogous formulation of the embedding problem for genus 3 does not  suffice for explicitly computing all primes of bad reduction. We introduce  a new problem called the Isogenous Embedding Problem (IEP), which we relate  to the existence of primes of bad reduction. We propose an algorithm which  computes effective solutions for this problem and exhibits a list of primes  of bad reduction for genus 3 curves with CM. We ran this algorithm through  different families of curves and  were able to prove the reduction type of  some particular curves at certain primes that were open cases in the  literature.