The full implementation of an EU entry-exit system introducing fingerprinting and facial recognition checks at ports and airports is expected to be delayed again amid fears over congestion and long queues.

Ylva Johansson, the EU’s home affairs commissioner, said recently that the new entry-exit system (EES) would be introduced on 10 November with a contingency of delaying it one week to 17 November.

Johansson had given member states until 5 September to provide the required declaration on their state of readiness.

It is understood three countries, France, Germany and the Netherlands, have written to her to say they will not be ready. They expressed concerns about the lack of testing of the system in the field, raising new questions about the target launch date, according to multiple sources.

Sources say UK transport operators were briefed by government officials last week to expect a further delay.

The introduction of the EES, which required non-EU citizens to have their fingerprints or photos taken before entering the Schengen area, has already been delayed twice. It was due to be introduced last summer but France expressed concerns it would have an adverse impact on the rugby World Cup last autumn and this summer’s Olympics.

It was then rescheduled for 6 October this year but put back until November amid concerns congestion would disrupt school holiday visits into the EU from the UK and other non-EU countries.

Several sources stressed that France, the Netherlands and Germany were “fully supportive of the checks” as it would increase security and speed up passport checks for non-EU citizens.

France’s main concern is congestion in Dover, where British and French border controls take place.

This year, Ashford borough council warned of a worst-case scenario involving delays of up to 14 hours affecting freight traffic and leisure or business car and coach travel.

One source in France said a “big bang” option on 10 November was just not viable, with expectations that it would be phased in over a year.

However, another said success would come only if all border posts were fully operational and recording every single entry and exit of a passenger.

The Port of Dover deals with three types of traffic – lorries, passenger cars and coaches. It is less concerned about checks of truck drivers because more than 80% of them hold an EU passport.

Checking passengers on the 68,000 coaches a year is more problematic but they will be directed through a new border control plaza. However, delays with the 1.6m cars that use ferries annually will have a knock-on effect on trucks and coaches because they all end in the same queue next to the ferry entry point.

The EES is being introduced at all entry ports and airports, with Germany concerned about the effect on smaller airports such as Cologne and Munich alongside Frankfurt, while the Netherlands has to deal with traffic from Schiphol, one of Europe’s busiest hubs.

Passengers will have their fingerprints or a photo of their face taken the first time they arrive in the EU after the introduction of the EES, with electronic verification of biometric data thereafter.

One UK source said: “They could start it but then phase in the time-consuming stuff like fingerprinting, but also give operators such as the Port of Dover the freedom to freeze checks if they see queues building up. This is all about capacity to manage congestion.”

A source in France said: “The problem is the testing has been desktop. We need live testing. Everyone is now waiting for the response of the commission.”

Some feel it is unlikely the commission will backtrack, having announced the launch date so recently, but equally, officials cannot ignore the concerns of the three countries which manage some of Europe’s biggest hub airports.

“This is what happens when politics hits the real world. Countries have to commit to launching and as the time gets closer and closer they are not willing to sign up to something they cannot deliver,” said a source.

The commission was approached for comment.