The Lithuanian Prosecutor General's Office said on Monday it had received the US response to its request for international legal assistance sent in September.
The US bodies said in the response that "the United States is not in a position to provide the requested data and answers to Lithuanian prosecutors' questions," the office said in a press release.
The prosecutors are continuing their pre-trial investigation "in accordance with the established plan for the investigation and procedural actions," it said, adding that all the circumstances relevant in the probe "can only be ascertained after all the necessary data are collected".
The US Senate in December 2014 published a report on secret CIA detention sites. Human rights activists believe that one of the sites, the one referred to as "Violet" in the report, was located in a building in Antaviliai, near Vilnius, between 2005 and 2006.
The Prosecutor General's Office has not yet named any suspects in its pre-trial investigation regarding illegal transportation of people across the national border and abuse of office, which has been underway since 2014.
The prosecutors say they have sent requests for legal assistance to the United States, Poland, Romania and other countries as part of the probe.
They say some of the countries have responded, but "no significant data for the investigation has been received so far".
They would not provide any details about the investigation, saying all information is classified as a state secret or an official secret.
The European Court of Human Rights (ECHR) ruled on May 31 that the CIA had operated a secret detention site for terror suspects in Lithuania between 2005 and 2006.
Lithuanian government officials told the Strasbourg-based court that the building in Antaviliai had been "an intelligence support center" and that the suspected planes had transported communication equipment rather than people to Lithuania.
The ECHR is expected to announce on Tuesday whether or not to accept the Lithuanian government's request to reconsider the judgment.