The Indonesian language (Bahasa Indonesia) has a number of uncommon characteristics, such as a great amount of derivational affixes. There are so many combinations of affixes and stems in Bahasa Indonesia that ambiguities often arise. To record all words into a word dictionary is almost impossible because it will make the size of the word dictionary huge and processing time very long. We propose a method to analyze the morphology of Indonesian words by using part-of-speech (POS) tagged data, an affix rule table and minimum connectivity costs to solve the problems mentioned above. Experiments showed that our system achieved a good analysis result (more than 97% accuracy).