The European Commission has said that any delays at European airports due to stricter security checks are the responsibility of member states.
New European Union rules introduced following terror attacks in Paris and Brussels require countries to carry out more stringent checks on travellers entering and leaving the Schengen area, which allows passport-free movement across much of the EU.
The change means the details of passengers from non-Schengen countries, such as Ireland and the UK, are run through databases to alert authorities if they are known to pose a threat.
Passengers arriving at airports in Spain, Portugal, France, Italy and Belgium face immigration queues of "up to four hours", according to Airlines For Europe (A4E).
The group, which represents carriers including easyJet, Ryanair and British Airways' parent company IAG, claimed some passengers are missing their flights because of the issue.
The EC said that member states have had time to prepare for the tighter controls which were brought in following the Paris terror attacks in November 2015.
Commission spokesperson Mina Andreeva said: "This is about the security of our citizens. All EU member states wanted the current rules. They asked for them specifically.
"Every member state agreed to them, so the rules we have are very clearly there to protect the security of our citizens.
"More checks can lead to more delays, and that is the price for security. We cannot have on the one hand a joint request from member states to have more checks and controls, to increase security, and the same time have complaints about longer waiting periods."
Following the Paris attacks EU member states sought tighter passport controls at air and sea ports.
This was in response to concerns that foreign fighters, who were EU citizens, were able to exploit weaknesses in the system in order to cross borders within the EU's passport free Schengen system.
A change in the rules required passengers moving in and out of the system to have their passports checked against a broader range of data bases, such as the Schengen Information System (SIS) and Interpol's database on stolen and lost travel documents (SLTD).
All third country nationals are subject to the checks, but following the new rules, EU citizens who are entitled to free movement can also be subject to checks.
Member states do have discretion to apply more targeted checks if they affect traffic flows, but only until 7 October 2017.
"It was clear that member states had time to prepare for these new rules presented by the Commission in December 2015," Ms Andreeva told reporters.
"The implementation of the new rules falls under the responsibility of the member states who need to ensure the deployment of sufficient resources and also staff in order to make these checks as smooth as possible."