Qantas chief executive Alan Joyce’s pay increased by $287,000 in the past year amid delays, cancellations and other problems that have plagued the airline and damaged its reputation, the company’s annual report reveals. The total value of his pay packet rose from $5,288,000 in 2021 to $5,575,000 this year, mainly because Joyce’s base pay returned to its pre-pandemic level of a little over $2.1m after two years in which he voluntarily took a cut due to the Covid-19 pandemic, which grounded the airline’s fleet of planes. However, Joyce did not receive a bonus this year, as the scheme was suspended and will not return until next year. The report, filed with the stock exchange on Friday, also shows the Qantas board has decided to rejig the pay packages of Joyce and other senior executives so that short-term bonuses better reflect customer service and the airline’s reputation. Qantas needs “to do more to deliver the service our customers expect”, the chair of the board’s remuneration committee, Jacqueline Hey, said in the report. She said the new bonus scheme will “prioritise a combination of key operational measures like punctuality and reliability of our airlines, customer satisfaction … and the group’s reputation and trust, to align executive incentive outcomes to our customers’ experience”. Sign up to receive an email with the top stories from Guardian Australia every morning A Qantas spokesperson disputed Guardian Australia’s use of statutory total figures provided in the company’s annual report, which include estimates of the value of Joyce’s potential future entitlement to shares, as “not an accurate figure of what he got paid”. The spokesperson said that Joyce’s take-home pay for 2022 was $2.27m, up from $1.98m in 2021, but 77% below pre-Covid levels. Both Qantas and its budget subsidiary, Jetstar, have been plagued by delays, cancellations and other problems as air travel bounced back from the pandemic this year. Joyce was forced to apologise after blaming customers for not being “match fit” to fly as queues snaked around airports in April. The Australian Competition and Consumer Commission this week said it was investigating Qantas over customer complaints about late and cancelled flights, and is continuing an existing investigation into the company’s policies toward refunds and flight credits. About 4,000 Australians were stranded in Bali for a week by Jetstar after the budget carrier cancelled eight return services to Denpasar airport. And on Wednesday night customers on a Qantas flight from Sydney were escorted off the plane by armed police when it landed in Melbourne because at least one passenger boarded without going through security screening. Qantas has been scrambling to hire more workers after laying off thousands during the pandemic but says a tight labour market has made this more difficult. In addition to receiving no short-term bonus this year, Joyce also received no Qantas shares under the company’s long-term incentive scheme, although his entitlements under this arrangement remain alive. Under the scheme he would have been entitled to about 1m shares in Qantas, worth about $5.25m at current prices, accrued this year and under previous bonus schemes stretching back to 2018. However, Joyce “offered, and the board agreed, to defer the decision until at least August 2023,” Qantas said in the annual report.