Victoria's Ombudsman will investigate the fairness of the state's public transport fines regime after a rise in complaints from commuters.

The probe will focus on the measure that allows passengers without a valid ticket to pay a smaller $75 on-the-spot fine if they waive their right to appeal.

Commuters without a valid ticket can pay the on-the-spot penalty, or they may be issued with a greater fine of $223.

The investigation will look at how penalty fares are issued and the complaints process for those wanting to dispute a fine.

Last financial year the Public Transport Ombudsman saw a 43 per cent increase in complaints about transport fines.

Separately, the Ombudsman said of 490 complaints it received between August 2014 and December last year, almost 80 per cent centred around fare enforcement and the discretion used by public transport officers in issuing fines.

Last month the State Government said it would review myki fines, saying the enforcement of the ticket system needed to be fair.