The drivers switched their meters to a higher rate used when trips go into Nassau and Westchester counties, even though they were still in the city.
On Wednesday, there was a hearing to get to the bottom of the problem.
"To a large extent in this case, the horse has been let out of the barn," transportation chairman James Vacca said.
Vacca pulled in TLC leaders and fellow Council members to find out how this happened for as long as it did.
"We are insisting that the public be told in a very clear and forthright way exactly what happened," Vacca said. "What was the extent of any of the illegalities that may or may not have taken place?"
"Be sure the majority of drivers are honest hard-working men and women giving top notch service to city residents and visitors every day," TLC commissioner David Yasky said.
Cabbies say don't let a few bad apples ruin the bunch. They believe they deserve an apology.
"The people don't pay me," driver Osman Chowdhury said. "They say you cheating me. Three times happen the last three days. It's very painful to me."
For its part, the TLC has come up with a solution - big brother. There will now be an alert that tells passengers when the higher rate is in effect.
TLC leaders are also working to figure out which drivers deliberately overcharged passengers, and plan to strip the guilty of their hack licenses.
This week, about one-third of the city's 13,000 yellow cabs were equipped an alert system telling passengers if the higher rate is activated. The commission hopes to install the rest over the next week.
Passengers are welcoming the change with open arms.
"I felt like I was being robbed years ago, so I stopped taking them a while back," Hollis resident Ninoska Etienne said.
"I always try to see if I'm being overcharged, but you can't always know," Far Rockaway Resident Deborah Leben said. "Of course, I don't think it's fair, but sometimes you're desperate and you need to get in that cab and they know it."