Brussels says China is blocking imports from European Union countries when they contain components from Lithuania.
Vilnius and Beijing are in a dispute over Taiwan.
Valdis Dombrovskis, the European Commissioner for Trade, said in an interview published on Friday in Germany's Die Welt newspaper that Brussels is "concerned" over the latest development.
"We now know of many cases where imports from Lithuania and the EU are blocked in Chinese ports, and the number is increasing every day," he said.
"Apparently, Chinese customs refuse to clear goods from other EU countries if they contain parts from Lithuania.
"This ranges from small shipments to very large ones. There is also a wide range in terms of the amounts involved. Given the huge volume of daily trade between the EU and China, it is not surprising that this figure is growing very fast."
The EU recently announced that it was in contact with the Chinese authorities "to quickly clarify the situation" regarding blockades of goods from Lithuania, and said it was considering filing a complaint with the World Trade Organization if necessary.
Vilnius accuses Beijing of blocking its products at customs to protest against the opening in July of a Taiwanese diplomatic representation in the Baltic state with the name "Taiwan" instead of the usual "Chinese Taipei".
China is reluctant to use the word Taiwan officially, fearing that it would help give international legitimacy to the island, which it considers part of its territory.
Lijian Zhao, the spokesman for the Chinese Foreign Ministry, denied that Beijing is not clearing customs for Lithuanian products at a regular press briefing on Wednesday.
"The claims that China's authorities 'are not clearing Lithuanian shipments' and that 'they are rejecting import applications from Lithuania' is not true," he told reporters. "If companies face technical problems in exporting certain products to China, they can report to competent Chinese authorities through normal channels."
The US Secretary of State said in a readout of a call with Lithuanian Prime Miniter Ingrida Simonyte on Tuesday that China allegedly not clearing Lithuanian shipments or shipments with Lithuania components "appear to constitute a form of economic coercion".
He offered "US support for Lithuania in the face of these actions and reaffirmed the US commitment to work with like-minded countries to push back against the PCR's (People's Republic of China) coercive diplomatic and economic behaviour".
The EU's top diplomat, Josep Borrell, also stressed earlier this week that the 27-country bloc "will stand together against all political pressures and coercive measures applied against any of its members."
Zhao, however, said that "the Lithuania side bears the sole responsibility for the severe difficulties in China-Lithuania relations" and affirmed that "China doesn't bully or wantonly sanction others, wield long-arm jurisdiction or suppress foreign businesses".
"What Lithuania should do is face the crux of the difficulties in the relations with China, reflect upon itself, and admit and seriously correct mistakes, instead of soliciting US' support. The US should be objective and unbiased, and stop distorting facts and fanning flames," he added.
Beijing had already announced on November 25 that it was stopping issuing visas to Lithuania, four days after it had already cut trade and diplomatic ties with the Baltic country.
Vilnius, meanwhile, is among the countries to have announced a diplomatic boycott of the 2022 WInter Olympics held in China over the country's human rights track record.