Customs did not give a reason for the suspension.
The agency typically halts imports of meat if exporting nations report outbreaks of disease in livestock. Lithuania has not reported any animal disease to the World Organisation for Animal Health (OIE) recently.
The move comes, however, after Britain said on Monday it will join the United States and Australia in backing an EU trade case against China at the World Trade Organisation over Beijing's alleged trade curbs on Lithuania.
The European Commission says Lithuanian exports to China fell 91 per cent in December compared to the same month in 2020.
Lithuania allowed Taiwan to open a de facto embassy in its capital Vilnius last year, angering Beijing which regards the self-governed island as its own territory.
Taiwan's Foreign Ministry condemned the latest Chinese move, which it called "unilateral" and "bullying" and the latest example of Beijing trying to change Lithuania's foreign policy.
"We firmly stand together with Lithuania," ministry spokesperson Joanne Ou told reporters.
China is the world's top importer of beef but shipments from Lithuania are minimal, at less than 2000 tonnes in 2020.
Taiwan has stepped up its food imports from Lithuania to help ease the impact of Chinese curbs, most recently rum.
The first batch of 1200 bottles sold out in less than an hour after going on sale this month.
