"On 31 January 2012, we received the application for temporary residence, the case is being processed," Irena Merkienė, director of the department's General Affairs Division, told BNS.
Avakov, former governor of Ukraine's Kharkov region, is an associate of the country's convicted ex-PM Yulia Tymoshenko.
Avakov was detained in Italy in March but was released. An Italian court plans to decide on his extradition, Reuters has reported. The information was also provided to BNS by Avakov's Lithuanian friend Audrius Butkevičius.
"A Rome Court of Appeals released him on 10 April after finding nothing but political reasons behind his detention. Another hearing will be held to decide on his extradition," Butkevičius, politician and former defense minister, told BNS in a telephone interview from Italy on Friday.
Butkevičius who has been sentenced for attempted fraud said that Avakov was his friend whom he has known for the past two decades.
In his words, Avakov is currently in Italy.
Asked whether Avakov intended to apply for political asylum, Butkevičius replied: "I think it is a matter he should consider. However, I cannot answer the question for him."
A report about Avakov's application for residence in Lithuania was issued by Russia's news agency Interfax, citing chief prosecutor of the Kharkov region, Oleksandr Babkov.
In the prosecutor's words, Avakov told Lithuanian institutions that he was employed in a Lithuania-registered company Divia Investment that was established by his wife.