"What I want from the pre-trial investigation conducted by prosecutors is that they use all possibilities (...), all means of evidence here, within the country," he told reporters on Thursday.
Skvernelis said that actions by law-enforcement bodies cannot be limited to formal request for legal assistance.
The state needs answer to questions on whether responsible officials had their decisions approved by the country's top political leaders and where funds allegedly received were spent, he said.
The government several days ago appealed the European Court of Human Rights' ruling that a Saudi Arabia-born Palestinian was unlawfully interrogated at a secret CIA detention site in Lithuania more than a decade ago.
The ECHR ruled in late May that Lithuania hosted a secret CIA prison for terror suspects between 2005 and 2006, ordering the country to pay 130,000 euros in damages to Abu Zubaydah over his alleged unlawful imprisonment in Lithuania.
In a reversal of the Justice Ministry's earlier announcement that Lithuania would not turn to the Grand Chamber, the full Cabinet decided to ask for the judgement to be reviewed.
The Lithuanian government's representatives told the Strasbourg-based court that the suspected building in Antaviliai, near Vilnius, had been intended to be used as an intelligence support center and that the suspected planes had transported communication equipment rather than people to Lithuania.
Some human rights activists believe, however, that Lithuania hosted a detention site referred to as "Violet" in a US Senate report.
The document says that the CIA offered an undisclosed amount of millions of dollars to "show appreciation" for supporting the program.