A mining town GP has been found in breach of the 80/20 rule despite claiming that he was often the only fully registered doctor available in his rural community swamped by thousands of fly-in, fly-out workers.

Dr Manukharan Nithianantha is likely to be forced to repay thousands of dollars in Medicare rebates after losing his Federal Court appeal against the Professional Services Review (PSR).

The GP in the central Queensland town of Blackwater, 800km north-west of Brisbane, had challenged a finding by the watchdog that claiming more than 80 MBS services on 28 days between May 2013 and 2014 could not be justified by exceptional circumstances.

He argued that the high billings were a consequence of running one of just two practices in the town, where other doctors were working limited hours and under conditional registration.