"I think it was not the opening of the Taiwanese office that was a mistake, but the name, which was not coordinated with me," he told the Ziniu Radijas radio station.
While both Lithuania and Taiwan can open representative offices that do not have diplomatic status, "the name of the office became a key factor that now has a very strong impact on our relations with China", according to Nauseda.
"I believe the name was the spark, and now we have to deal with the consequences," the president said.
"Unconventional measures have started to be taken against Lithuania, and we have to be very active and signal very clearly to the EU that this is an attack, a kind of pressure on one of the EU countries," he added.
Tensions between Vilnius and Beijing surged last year after Vilnius allowed Taipei to name its representative office "Taiwanese".
Elsewhere in the world, Taiwan's representative offices operate under the name of Taipei, in line with an international consensus that this does not run counter to the "one China" policy which prevents Taiwan from being treated as a separate state.