Worrisome issues pointed out by the auditors include a non-working mobile phone blocking system at the Alytus correctional facility, unused criminal intelligence equipment, and suspicions that former top officials of the Justice Ministry provided false information to the Finance Ministry.
According to Jankevičius, the Prison Department's unit that was set up to ensure the prevention of corruption failed to do so.
"The failure to see the processes that were underway was either a sign of incompetence or a sign of malice," he said.
Deputy Justice Minister Ernestas Jurkonis said that steps have already been taken to tighten up internal controls at detention facilities.
Both scheduled and unscheduled searches were conducted in all detention facilities last week to get an objective picture of how the controls of prohibited items is working in prisons.
"I can say that we'll have to work seriously with the Prison Department, because the situation is not satisfactory. Every search finds prohibited items, (such as) prohibited communication devices, and inmates in a state of drug and alcohol intoxication," he said.