The FTC wants to look into possible antitrust issues stemming from the deal, the New York Post first reported on Saturday, quoting anonymous sources. The Wall Street Journal's AllThingsD technology blog later got a confirmation from Google about the probe.
Neither Google nor the FTC immediately responded to a request for comment.
Earlier this month, Google announced it had acquired Waze, a crowdsourced mapping application developer based in Israel, saying it wanted to add more real-time navigation tools to its Maps product.
According to the New York Post, Google didn't voluntarily submit the deal for FTC review because Waze's U.S. revenue was less than $70 million.
The FTC is reportedly getting involved because, with the deal, Google, a dominant player in the online mapping market, swallowed one its few viable competitors.
The companies didn't disclose financial details of the deal, but various reports at the time put its value at anywhere between $1 billion and $1.3 billion.
The Waze mobile app lets users share reports about road and traffic conditions in real time, so that other motorists can make route adjustments.
"We're excited about the prospect of enhancing Google Maps with some of the traffic update features provided by Waze and enhancing Waze with Google's search capabilities," Brian McClendon, Google's Vice President, Geo, wrote in a blog post announcing the deal on June 11.
McClendon also said that the Waze development team would remain in Israel and operate separately "for now."
Before Google swooped in and snapped up Waze, other companies had reportedly been interested in the company, including Facebook and Microsoft.
The application had about 50 million users at the time of the Google deal, Waze said in its own blog post about the deal.
Waze leaders decided against taking the company public, and then evaluated "many options" before agreeing to the Google deal, Waze CEO Noam Bardin wrote in that blog post.