President Dalia Grybauskaite described the fire as "unbelievable and shocking".
Prime Minister Saulius Skvernelis called the cathedral "a symbol of the whole Christian Europe" and Foreign Minister Linas Linkevicius said it was "devastating" to see the historic Paris landmark engulfed in flames.
"Unbelievable and shocking. We pray for #NotreDame," Grybauskaite said on her official Twitter account.
Skvernelis said on his Facebook page that it was "horrible" to see Notre-Dame, "a symbol not only of Paris but also of the whole Christian Europe", being devastated by the fire.
"Devastating to see the burning #NotreDameDeParis. My thoughts are with Parisians and the people of #France as the symbol of #Paris and a pearl of world gothic is at serious risk of being destroyed," Linkevicius tweeted.
"Nothing can destroy our love to beautiful Paris," he added.
Firefighters said in the early hours of Tuesday that the fire was completely under control but not totally extinguished yet.
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