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Health minister Salvador Illa said the database won't be shared publicly and will be kept in accordance with data protection rules.
According to The Local, Illa said during an interview with La Sexta television: "What will be done is a registry, which will be shared with our European partners... of those people who have been offered it and have simply rejected it.
"It is not a document which will be made public and it will be done with the utmost respect for data protection."
He went on to say employers or other members of the public would not be granted access to the list.
Illa stressed that the best route out of the pandemic was to vaccinate as many people as possible.
He added: "People who decide not to get vaccinated, which we think is a mistake, are within their rights.
"We are going to try to solve doubts. Getting vaccinated saves lives, it is the way out of this pandemic."
Vaccinations are not mandatory in Spain, but according to a recent poll, only 28 percent of Spanish residents have said they would be unwilling to take it.
The Local reports that by June the government is expecting between 15 million and 20 million people to have been vaccinated.
Covid-19 vaccines are now being rolled out across European Union, after the EU approved use of the Pfizer-BioNTech jab.
To celebrate its arrival in Germany, pilot Samy Kramer drew a, very impressive, syringe in the sky using his flight path.
He mapped out how the route would need to be taken on a GPS device, before flying in the skies above Lake Constance, southern Germany.
It created a syringe-shape, which showed up on flightradar24.
Speaking to Reuters, 20-year-old Kramer said: "There are still relatively many people opposing the vaccination and my action may be a reminder for them to think about the topic, to get things moving.
"Perhaps it was also a bit of a sign of joy, because the aviation industry has been hit pretty hard by the pandemic."
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