The Democratic governor is using his amendatory veto power to tweak the legislation sent to him after months of debate and negotiation over the measure.
"I have examined this particular bill over the last couple of weeks very carefully and there are serious flaws in this bill that jeopardize the public safety of the people of Illinois. Therefore I use my power to make common sense changes," Quinn said during a press conference Tuesday.
The state is in the process of complying with a federal appeals court order to undo Illinois' ban on carrying concealed weapons in public. The court ruled in December that it was unconstitutional for Illinois to ban the public possession of concealed firearms. The deadline to comply is July 9.
Quinn, who is a big advocate of gun control, says he never agreed with the court's ruling and the bill lawmakers sent him is flawed and needs changes.
Some of the changes include limiting the amount of guns someone can carry, as well as limiting the number of rounds that can be carried.
The legislation permits qualified gun owners who pass background checks and undergo 16 hours of training to get permits for $150.
Some experts weighed in on the controversial debate.
"Anything he vetoes out of that bill or changes is going to take the right of self-defense away from law-abiding citizens," said Richard Pearson, executive director of the Illinois State Rifle Association.
"I think he is trying to show that he is out in the interest of protecting public safety and he is a champion for public safety over and above everyone else. That's the message I think he's trying to send," said Laura Washington, ABC7 political analyst.
Meanwhile, because the bill passed with huge majorities in the Illinois House and Senate, Quinn's actions are setting up a showdown in Springfield- where his changes are likely to be overridden.
A spokesperson for Illinois Senate Republican leader Christine Radogno told ABC7 that they will hope for just that. The spokesperson added that the governor has ignored a bi-partisan compromise which has led to frustration.
The Associated Press contributed to this report.