Virgin Australia passengers complained to the airline ombudsman more often than Jetstar passengers last year, new figures show.

The industry-funded Airline Customer Advocate's 2016 annual report shows Tigerair again received the highest rate of complaints across the top-five most complained about issues out of Australia's four largest carriers.

Tigerair received 31.9 complaints for every million passengers over refunds, delays and cancellations, baggage services, fees and charges, and airport customer services, the report shows. That is down from 37.7 complaints per million passengers in 2015.

Virgin Australia, Tigerair's full-service sister carrier, was the subject of 13.5 complaints about those issues per million passengers carried, up from 10.5 in the prior year.