The move prompted China to restrict diplomatic contacts with Lithuania and stop issuing visas.
Lithuania's President has said the decision to allow Taiwan to open a representative office in Vilnius under its own name was "a mistake".
Gitanas Nauseda told a local radio station that he was not consulted about the move, which has heightened tensions with China.
Beijing claims Taiwan as part of its territory and does not give diplomatic recognition to nations that treat the island as a separate state.
The opening of the representative office prompted China to restrict diplomatic contacts with Lithuania in November and stop issuing visas to the country.
Lithuanian companies have also complained about complicated trade restrictions when doing business with China.
"I think it was not the opening of the Taiwanese office that was a mistake, it was its name, which was not coordinated with me," Nauseda told Ziniu Radijas.
"The name of the office has become the key factor that now strongly affects our relations with China," he added.
The representative office bears the name Taiwan rather than Chinese Taipei, which is used by many foreign nations to avoid offending China.
Taiwan has just 15 formal diplomatic allies but maintains informal ties with all major nations through trade offices that act as de facto embassies.
As President, Nauseda oversees the country's foreign policy and represents Lithuania at European Union summits.
But Nauseda supported other officials in labelling China's response to the representative office as undeclared "sanctions".
"Unconventional measures against Lithuania have started to emerge," he said on Tuesday.
"We have to be extremely active and make it very clear to the European Union that this is an attack, a kind of pressure on one of its member states."
Lithuania plans to open its own trade office in Taiwan later this year. The EU member state has also closed its Chinese embassy over the dispute and pulled its last diplomat from Beijing.