A diplomatic row between Lithuania and Austria erupted after Austrian authorities released a former KGB officer implicated in a 1991 massacre in Vilnius.
Mikhail Golovatov was arrested at Vienna airport on July 14 but released after 24 hours and allowed to travel to Moscow.
A Justice Ministry spokeswoman said Austrian authorities had decided that the arrest warrant issued by Vilnius, which alleges crimes against humanity, lacked details of the man's suspected criminal actions.
Lithuanian Deputy Foreign Minister Asta Skaisgiryte Liauskiene said the country had recalled its ambassador from Vienna and delivered a protest note.
"Today in the morning, the Austrian charge d'affaires in Vilnius was called to the [Lithuanian] Foreign Ministry where we handed him a note asking him to present the Austrian side's explanation why such a hasty decision to release the suspect in the January 13  case was taken by Austrian authorities."
Golovatov allegedly took part in the storming of the Vilnius TV tower by Soviet special forces, which left 14 dead and hundreds injured.
Lithuanian Foreign Minister Audronius Azubalis was raising the issue on July 18 at a meeting of EU affairs ministers.
Meanwhile, a crowd of protesters assembled outside the Austrian Embassy in Vilnius, shouting "Shame on Austria!"
compiled from agency reports