Digital Covid-19 certificates aimed at facilitating free movement in the European Union came into force across the bloc on Thursday, a long-awaited milestone for countries hoping to boost their ailing tourism industries — but also a point of friction over the number of vaccines that do not qualify.

Free movement is a key pillar of European integration, and E.U. officials said last month that the certificates would “again enable citizens to enjoy this most tangible and cherished of E.U. rights.”

So far, the European Union lists four vaccines as qualifying for the certificate, all of which have been authorized for use across the bloc. They are the vaccines made by Pfizer-BioNTech, Moderna, Johnson & Johnson and AstraZeneca.

That leaves out a vaccine that the international Covax mechanism has distributed across Africa: Covishield, a version of the AstraZeneca vaccine that is manufactured in India. It is, however, accepted in a handful of E.U. member nations.

Without naming the E.U., the Covax facility on Thursday urged “all regional, national and local government authorities to recognize as fully vaccinated” all people who have received a vaccine approved by the W.H.O. when easing travel restrictions, warning that not doing so would create a two-tiered system.

Through a Q.R. code issued by their country of residence, certificate holders will be able to show that they have been either fully vaccinated, tested negative or have immunity after a recent recovery. That will exempt them from most travel or quarantine restrictions.

Many European governments have already eased such rules, and each member nation can still revive protective measures if a country’s health situation deteriorates. Germany, for instance, has imposed restrictions on travelers coming from Portugal, which has faced a surge of new cases driven by the spread of the Delta variant.

While countries have agreed that national health authorities will issue the certificates — most E.U. countries have already been doing so — they are divided over who should check them, where and when.

Citing privacy concerns, Germany and Austria have not given airlines access to verification devices that they would need to scan the Q.R. codes. France has distributed such tools in airports, and Spain has built a system whereby Q.R. codes can be checked before passengers travel to the airport.

And one country, Ireland, has yet to set up a verification system for the digital certificates, after its national health system was recently targeted by cyberattacks, according to E.U. officials.

The divergences have highlighted the challenges that the E.U. faces in allowing free movement across the bloc.

This week, a group of airlines and airport representatives urged member states to set up verification systems before departure — alongside online check-ins, for instance — to avoid chaotic situations at airports upon arrival.

Echoing some concerns shared by the travel industry, the European Commission, the bloc’s executive arm, noted that the 27 E.U. member states had planned more than 10 verification processes.

“The digital Covid-19 certificate is an important tool that ideally will give people confidence in the easing of travel restrictions,” said Thomas Reynaert, the managing director of Airlines for Europe, an organization based in Brussels that represents the bloc’s largest carriers. “But this can only work for travelers if member states implement it in a harmonized way.”

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