"Europe is open for [the] Ukrainian people, but not necessarily for this government," Grybauskaite said.
Lithuania holds the rotating presidency of the European Union. Radio Free Europe/Radio Liberty said she was speaking from Brussels where EU leaders are discussing what comes next after Ukraine suspended efforts to move closer to Europe.
The Ukrainian government in November suspended efforts to sign free trade and association agreements with the EU, saying the agreement could jeopardize its economic ties to Russia.
Pro-EU protesters have flocked to the streets of Kiev to protest the government's decision.
European Council President Herman Van Rompuy said at the Brussels meeting the agreements were still open for Ukraine's signature as soon as the country is ready, RFE/RL reported.
The Ukrainian government said it wasn't abandoning the EU measure altogether. The BBC reported President Viktor Yanukovych said the overall issue was a domestic matter.
"What is very important is that this is our internal matter, and that other countries do not intervene in our internal affairs," he said.