The theft investigation originated from an internal TTC investigation about missing money.
The audit found that the accused TTC collector’s float was approximately $3,800 short.
The employee allegedly tampered with TTC token rolls in order to cover for the theft and then went to two union representatives for help.
Police say the two union representatives then allegedly helped destroy evidence.
All three men from Toronto surrendered to police Tuesday.
Deodato Souda, 54, is charged with theft under $5,000.
Both John Wales, 63, and Clarke Smith, 53, are charged with compounding an indictable offence, theft under $5,000 and breach of trust.
The three will appear in court on Jan. 9, 2013.