Renatas Požėla, commander of border guards currently working under a tightened regime, said the majority of fans were Russian citizens.
Additional trains for fans were launched on Friday night ahead of a match between Serbia and Switzerland.
"There were around 500 people in each train and there were five trains this night," Požėla told BNS Lithuania. "60-70 percent of them were Russian citizens, 15 percent were Serbs and there were also Belarusian, Moroccans and Americans."
Football fans in mainland Russian travel to Kaliningrad by train as trips are free for those having Fan IDs.
Lithuanian border guards also on Friday blocked two citizens of Algeria from entering the country as one of them had no valid Schengen visa and the other one had fake documents. All in all, Lithuanian border guards have stopped 14 foreigners with Fan IDs from entering Lithuania ahead of and during the World Cup.
Officers are concerned that third-country citizens are using the opportunity of free travel in Russia to eventually reach EU countries.
"Some fans are taking advantage of the championship, and tension is already rising on the Polish-Belarusian and Polish-Russian borders. They already see it as a threat, (…) so we should not feel calm as well," Požėla said.