Chicago Mayor Rahm Emanuel said Wednesday he will review a city program that funnels public money to non-profits, after the city’s inspector general this week revealed that a group led by Chicago’s former first lady disproportionately benefited from the program.

But Emanuel stopped short of commenting in on the merits of the report, which found that After School Matters, founded by former Mayor Richard Daley’s wife, Maggie, may have received preferential treatment by the city.

The report by Inspector General Joseph Ferguson found After School Matters received $915,000 in subsidies through the city’s tax increment financing program, or TIF. The money comes from cash contributions made by companies who benefit from the TIF program.

Fifty-nine percent of TIF agreements that benefited non-profits between 1985 and 2009 went to After School Matters, the report found. But it said the city unilaterally decided which non-profits would get that money, and found that, when asked, city officials could not explain how non-profits were chosen for the benefit.

After Wednesday’s City Council meeting, Emanuel maintained that after school programs are important and that TIF is a crucial economic development tool. But he didn’t weigh in on the report’s politically-touchy suggestions of favoritism toward Maggie Daley, who has been battling cancer.

“What I don’t want to see happen is, because of one report, that we shut down after school activities that will be - affect everybody’s neighborhoods and their children,” Emanuel said.

The city will look into whether TIF is the appropriate way for corporations to give money to non-profits, Emanuel said.

Meanwhile, Ald. Scott Waguespack (32) said he’ll introduce an measure to cancel or suspend any existing TIF agreements that funnel money to non-profits until the system is reformed, adding that he’ll work with the mayor’s office on changing the program.

“Let’s sit down, let’s determine how one of these not-for-profits could get this money, and let’s put a set of criteria together like they do for just about anything else,” Waguespack said.

Waguespack said the process by which non-profits are awarded the grants needs to be more transparent and should include caps on the amount of money that can go to any single group.