While audit costs will vary depending on the scope of the audits and other considerations, they are a small fraction of election administration costs.
For instance, the cost to retrieve and audit ballots for the November 2017 Coordinated Election in Arapahoe County, Colorado (about 350,000 registered voters) was approximately $500 for auditing 516 ballots; the audit followed the best practices recommended in this document. The county tabulated ballots centrally. There were approximately 93,000 ballots cast in that election.
This cost does not include the one-time development cost for the RLATool software utility (now available free of charge under an open source license) or expenses tied to ballot imprinting, ballot storage and organization, or other overhead expenses.
(Adapted from Principles and Best Practices for Post-Election Tabulation Audits, 2018)