"It is suggested that Lithuania should accept 207 displaced persons," the Representation said in a statement.
The proposed scheme envisages relocating 20,000 displaced persons in the European Union each year, distributing the number among member states based on their ability to integrate the newcomers as calculated using factors like population, GDP and unemployment rate.
Lithuania would be expected to shoulder 1.03 percent of the refugees, or 207.
Most would be resettled in Germany (15.43 percent or 3,086), France (11.87 percent or 2,375) and the United Kingdom (11.54 percent or 2,309).
Latvia would be expected to accept 220 displaced persons, Estonia 326 and Poland 962. The priority regions for resettlement will include North Africa and the Middle East.
The European Commission would contribute to the scheme by making additionally available a total of 50m euros for 2015 and 2016.
EU member states have so far accepted refugees voluntarily and their applications have been examine in the countries they have come to.
Brussels suggests creating in the future a "relocation mechanism" under which Lithuania would have to process 1.16 percent of asylum applications received in Europe.
The Commission proposal is aimed at reducing the existing burden for southern European countries in dealing with refugees coming from Africa.
Tensions are also rising because of the fact that the UK, Ireland and Denmark can opt out of the scheme under prior agreements.
EU leader are set to discuss the Brussels proposal in June.
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