"At this pace, the obligations to EU will not be fulfilled," Zilinskas told reporters at the parliament.
The interior minister added that there would be no sanctions in relations to the quota scheme.
"Lithuania is not the only country, which does not implement the obligations in full. Other countries face same problems as Lithuania does," he added, stressing Vilnius was not planning on accelerating the process of accepting refugees for security reasons.
In 2015, Lithuania pledged to take in 1,105 refugees over two years under the EU mandatory quota scheme aimed at relocating 160,000 arrivals among EU member states. Lithuania so far accepted 83 refugees.