The man was released in Vilnius after he filled out a form, the border police said. The man filled out the form as Marius Sablevicius, 21, and produced a valid passport.
The man was deported from Sweden because he had no way to make a living in the country. However, he jumped out of the Stockholm-Klaipeda ferry in Sweden's territorial waters April 20.
Staff of the Swedish Coast Guard saved the man.
Lithuanian daily Lietuvos Rytas reported that the real Marius Sablevicius lives in the Lithuanian town of Kedainiai and could not have jumped off the ferry. He said that his passport was missing.
Meanwhile, a spokesman for the border police said Sablevicius' passport was not listed in the department's database as missing or lost. The department has launched an investigation.