A Darwin-based Labor senator has had to repay taxpayers more than $17,000 for almost 40 wrongly claimed domestic flights, hotel charges, road tolls and taxi rides while travelling to Sydney for medical treatment.

An extensive Independent Parliamentary Expenses Authority audit of Malarndirri McCarthy's travel itineraries has on Thursday revealed multiple breaches of Commonwealth-funded travel expenses during a three-year period.

Senator Malarndirri McCarthy "self-reported" the travel expense claims. Credit:Alex Ellinghausen

The audit focus primarily on domestic travel connections through Sydney from July 2016 to April 2019.

The audit reveals Senator McCarthy herself had asked the parliamentary expenses watchdog to audit hundreds of travel claims since she was elected to Parliament, including claims for travel allowances and "especially my stopovers in Sydney".