The Seimas last spring changed the Law on Referendum to require fewer votes for amending Article 12 of Chapter 1 of the Constitution, which speaks about Lithuanian citizenship, than for amending other articles of that chapter.
The president refused to sign the amendments into law, saying that they might run counter to the Constitution.
If the president vetoes a law, the parliament must decide by voting whether to debate on the returned law anew or to consider it not adopted.
Some 107 lawmakers voted on Tuesday to consider the controversial amendments as not adopted and five abstained.
Currently, more than half of all citizens having the right of vote must say "yes" in a referendum to amend any article of Chapter 1. The Seimas had lowered the threshold for a referendum on citizenship to more than 50 percent of all voters who turn out, but no fewer than a third of all citizens with the right to vote.