Republican challenger Tom Schweich was leading Democratic Missouri Auditor Susan Montee with about two-thirds of the votes tallied.
Schweich is a former State Department official and first-time candidate for elected office. Montee was first elected in 2006 and is an accountant and lawyer.
Over the last four decades, just two sitting state auditors have lost their re-election bids.
The auditor's office was the only statewide post in Missouri government on the ballot this year.