One passenger told the BBC she waited for two hours at passport control, another said after a flight from Cork she waited so long they were put into another area.
Other passengers expressed their frustration on Twitter.
Sophie Elliot posted on the social networking site: "Last night at Stansted we were trapped in queues of over an hour - longer for the people behind us - cos 'a few planes landed early'."
More top news
The NHS could save over £8 million a year on dental treatment if all 12-year-olds chewed sugar free gum after meals, a study claims.
Older people in England are living longer than ever before, a new report has revealed.
Firms that fail to address the pay gap between male and female employees with be listed in new league tables.