The CBI has filed two charge sheets against Prabhakaran, who according to CBI sources had entered into a criminal conspiracy and obtained passports in the names of fictions persons. Prabhakaran then manipulated the particulars in the original passports and substituted photographs in the original passport for later use.

He had been providing fake passports to his associates for illegal migration, when the movements of Sri Lankan Tamils were monitored closely by the Indian authorities following the assassination of former Prime Minister Rajiv Gandhi. CBI officials had seized several such passports, created and manipulated by the accused. Though CBI could arrest some of his associates, they could not pick up Prabhakaran.