It’s alleged employees working inside subway station ticket booths pocketed the $3 fare after giving passengers change for cash transactions.
Spokesman Brad Ross says the TTC took action after customers raised concerns.
“We carry 1.7 million people every day, we can’t let two employees set the entire organization back, or to paint the entire organization with that brush," he said.
It’s not clear how much money may have been stolen but the alleged thefts date back a year and took place at subway stations across the city.
Two men — a 47-year-old and a 56-year-old — have been arrested and charged with a number of theft-related charges.
The news caps a tough week for the TTC.
On Tuesday CEO Andy Byford issued a YouTube apology for service delays that happened during Monday's afternoon commute. There were also two instances this week in which the doors of stationary trains opened while the train was away from the platform.