As a man living in exile, Nehemiah experienced the penalties that God had promised on his father's sins (Deuteronomy 28:64). The corruption of his own heart meant, however, that he could not rise above his father's sins as if he were somehow a better person. By his confessing his own sins, he indicates his desire to cease earning God’s judgment and to seek his mercy.
6 let your ear be attentive and your eyes open, to hear the prayer of your servant that I now pray before you day and night for the people of Israel your servants, confessing the sins of the people of Israel, which we have sinned against you. Even I and my father’s house have sinned.