This is the second similar case Lithuanian consular officials have encountered in past weeks.
A photograph published by the Foreign Ministry indicates that the passport, issued in 2011, features an entry Odessa Region/Russia.
The Lithuanian foreign minister's spokesman Kęstutis Vaškelevičius said the passport with an application for a facilitated transit document had been submitted to the consulate in Kaliningrad, but the consular officials did not accept it.
Last week, Lithuania's Foreign Ministry announced having refused a transit document to a Russian citizen whose passport specified Crimea/Russia as his place of birth.
Russia's federal migration authorities then dismissed the entry as a technical error.
"It is probably yet another mistake, although it is strange that everything has to do with Ukraine and the sensitive regions of Crimea and Odessa. Quite an odd situation. This can be referred to as mistakes, but it is strange that they are all in connection with a single country that is subjected to aggression. The coincidences say a lot. I do not want to make any further interpretations," Foreign Minister Linas Linkevičius told BNS on Thursday.
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