He said the data size of Jetstar passengers which included more than 100 respondents of the 11,000 overall was "around half the number of people we carry on one flight and a lot less than 34 million customers who flew with us last year."
"They also called it an international survey but only surveyed people from eight countries," he said.
Emirates took the crown as the best airline in the world. Tigerair was not included in the survey because the sample size of passengers was too small.
But Choice spokesman Tom Godfrey stood by the research and said "it's unsurprising Jetstar is disappointed in their poor performance but instead of trying to rubbish the survey, they should work on cleaning up their act.
"People are sick of poor treatment, particularly when flights are delayed or cancelled."
Jetstar said they continued to do "a lot of work behind the scenes on areas where we can improve, particularly on flight punctuality."
Customers rated airlines on a range of criteria including punctuality, checking in, boarding, treatment by staff, comfort on-board, meals, safety and value for money.