The 48 applicants for international protection were moved from Cyprus to Germany through an EU solidarity system for voluntary relocation, the Cypriot Interior Ministry said.
Last year the EU member reported the highest number of asylum applicants per capita and Cyprus says it is at the forefront of the bloc's irregular migration.
"This is the first of a series of transfers that will take place in the coming months," the ministry said.
It said the transfer was made "in co-operation with the European Asylum Service, the European Commission, the International Organisation for Migration and the German authorities".
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"This is the first relocation to my country but it is only the beginning, because Germany wants to take in more eligible persons soon to relieve the burden on Cyprus," ambassador Anke Schlimm said.
The Cypriot Interior Ministry said the EU had worked closely with member countries to ease the burden of irregular migration, especially among those considered "frontline states".
"Germany has accepted the relocation of 500 applicants," the ministry said.
"It contributes to addressing the migration challenges faced by the Mediterranean countries, especially Cyprus."
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The relocations are funded by the EU and the UN migration agency.
Nicosia claims that asylum seekers comprise six per cent of the island's population of 915,000, a record figure across the EU.
A total of 18,345 people had applied for asylum as of October, Interior Minister Nicos Nouris said earlier in December, compared with 13,325 for the whole of 2021.