Plans to fingerprint passengers entering the EU from 10 November are to be delayed for a third time after concerns were raised by France, Germany and the Netherlands, it has emerged.

The introduction of the entry-exit system (EES) requiring 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 in summer last year but France expressed concerns it would have an adverse impact on that autumn’s Rugby World Cup and this summer’s Olympics. It was rescheduled for 6 October this year, then put back again until November amid concerns about disruption to school trips into the EU.

EU diplomat sources said on Wednesday there was very little chance that any version of the new entry-exit system would be ready to be implemented in four weeks’ time despite an official announcement of its launch date by the European Commission last month.

EU capitals will be briefed on contingency plans at a meeting of home affairs ministers in Luxembourg on Thursday, with alternative options expected to be tabled.

One would involve a phased launch of the whole scheme port by port and airport by airport over months or even a year.

Another could involve an “EES Lite” being introduced next year at an as yet unspecified date, with data from passports uploaded to the central database but fingerprinting or facial recognition data taken elsewhere or at a later date. One of the big challenges at places such as Dover port is the delays caused by passengers having to get out of their cars, or bus, to have their fingerprints taken.

Another option is to change the EU rules that require biometrics to be taken at borders, allowing tourists and others to upload biometric data on an app or at secure locations away from the ports or airports.

One source said it was “a bit of mess”, with EU leaders trying to work out how to proceed without “losing face”.

France, Germany and the Netherlands are responsible for 40% of all inward traffic to the EU with major airports including Charles de Gaulle in Paris, Schiphol in the Netherlands and Frankfurt international hub in Germany, where there were also concerns about capacity in smaller airports including Cologne and Munich.

The three countries wrote to the European Commission in early September to say they could not sign a declaration of “readiness”, with France also concerned about holiday traffic from Dover in the UK at Christmas and the February school holidays. While talks have continued since then, no resolution has been found.

Sources say truck traffic is not the problem, as up to 90% of those driving vehicles across the Channel hold EU passports. But Dover port is concerned that any hold-up in passenger vehicles and tour buses could cause traffic to back up in the town and up the motorway.

It is understood that the cause of the delays centres on each country’s system for interfacing with the agency eu-Lisa, which manages the technology and databases for the bloc in the areas of free movement, security and justice.

“It is eu-Lisa which doesn’t seem to be ready yet. So that is a problem, and the commission will have to tell us how they see any way of accelerating it to such a degree that it will be possible to have it functioning before at 10 November, but I doubt it,” said one diplomat with knowledge of the issue.

“The problem is not on our side, it is on their side,” they added.