"Yes, it came from a third country, not a country in the European Union. I believe the authorities will soon specify it," Valkavičius told BNS Lithuania on Friday.
He confirmed that the information that has been published is about a crime that did not take place.
Representatives of the Lithuanian parliament have said that the false report sent to the parliamentary speaker and the police about an alleged rape could be an attempt to discredit NATO forces in Lithuania.
Parliamentary Speaker Viktoras Pranckietis and the Lithuanian police received the emails on Wednesday evening.
The Kaunas police said the data was wrong, launching a pre-trial investigation into misleading reporting or reporting of a crime that never occurred.
Pranckietis' spokeswoman said the letter told about German-speaking people surrounding a girl from the Jonava foster institution and raping her.
Germany started stationing troops in Lithuania in January. The troops will form basis of the international NATO battalion, which is being deployed in response of Russian actions in Ukraine and the Baltic Sea region.