Pranckietis visited the Chonhar checkpoint on the de facto border with the peninsula and was as close as around 100 meters away from Russian border guards.
"This is occupation and this is not Ukraine's problem. It is a war against Ukraine," the speaker told reporters.
Lithuanian diplomats say that this was the first visit by an EU official of such rank to the border with Crimea.
The speaker of the Seimas said that the West should make more active efforts for Crimea to be returned to Ukraine.
"The Minsk agreements do not even touch upon the Crimean issue. Therefore, we must think how to make the word 'Crimea' appear in future talks," he said, referring to a ceasefire deal for eastern Ukraine signed in Belarus' capital by Russian, Ukrainian, French and German leaders.
Russia annexed Crime in 2014 following the ouster of Moscow-supported Ukrainian President Viktor Yanukovych.