In return she dropped a lawsuit she had filed against the priest and the Tendai Buddhist sect to which he belongs.
"He has resigned as head priest and has repented, so we decided to come to a settlement," the woman's lawyer said.
Tendai officials were unavailable to comment on the case.
On four different occasions from December 2005 to May 2006, the old priest performed indecent acts on the woman, using the excuse of her needing to undergo purification to rid her body of eczema that was plaguing it and feeling her up.
In May last year, the woman sued both the priest and the Tendai sect, seeking 7 million yen in compensation. The priest resigned on Jan. 31. The woman agreed to end her litigation against Tendai as part of the settlement.