The association wrote to the European Commission this week regarding "challenges" with EES after a commission spokesperson reminded the 29 European countries participating in the scheme they have measures available to them to avoid delays.
The EU hopes to have EES fully operational by 9 April, although contingency measures will be available up to and throughout the summer, according to the commission spokesperson.
Abta said passengers' experiences of EES have been mixed so far, with some people having no issues whereas others have experienced queues or technical problems.