The process has stopped in recent months as the country had committed itself to relocating migrants until the end of 2017.
The date has now been extended to November 2019.
Migrants are being resettled under a mechanism approved by the EU in 2015 to share some 160,000 refugees among member states to help lighten the load on Greece and Italy.
Lithuania in 2015 pledged to accept a total of 1,105 refugees, but the figure was reduced to 1,077 on Wednesday, following adjustments made by the European Commission.
Some 468 people have been relocated to Lithuania so far.
"We are somewhere at the EU average," Interior Minister Eimutis Misiūnas said during the Cabinet's meeting.
However, most of the relocated refugees have left for richer European countries and only a small percentage of them have been returned to Lithuania.