EU Competition Commissioner Margrethe Vestager said Google's preferential use of its own shopping product in its search engine could be harmful to consumers and competitors.
Vestager announced the charges on Wednesday, five years after the investigation was launched.
"What I saw when I took office was that discussions about commitments didn't seem to move forward, neither very fast nor in promising way in order to finalize the case," she told reporters in Washington.
"It was my option that we should move forward here instead of waiting," said Vestager, who took office in November.
She also warned that the EU Commission on competition could also open investigations relating to other Google tools that may unfairly edge out competitors, including its travel, flights and hotel services.
"If an infringement is proven, and it's on purpose... a case focused on comparison shopping service could potentially establish a broader precedent for enforcing EU competition rules in other instances of Google favoring its own services over competing services," she said.
Google accounts for 90 percent of the online search market in Europe.
The concern is that competitors like travel portal TripAdvisor or business review Yelp could be squeezed out as a result of Google's dominance, prioritizing its own product over others in its search engine.
The California Internet company could face huge fines if found culpable -- as much 10 percent of its $66 billion in worldwide turnover last year -- and has 10 weeks to respond to the charges.
- Android abuse? -
Vestager said a second, separate investigation into Google's Android software has also been launched to determine whether the company requires smartphone manufacturers to pre-install Google apps and if it hinders them from developing their own services or apps.
She said the EU would work with various companies, including Google, to investigate the allegations.
"It is still way too early to give a timeline as to where our investigations will lead us or where it will end," she said.
US critics say the EU is being selective in singling out Google and other American companies, including Microsoft -- the target of an investigation a decade ago -- Apple, Facebook and Amazon.
The US Federal Trade Commission dropped its own probe of the company in 2013, saying it had done enough to meet complaints.
But Vestager said she wants to keep geopolitics off the table.
"I will do my best to make sure that it is not politicized, the Google case, and that it's not entangled in other issues," she said.
Speaking later at the Peterson Institute for International Economics, Vestager said the EU does not target US companies.
"In all our cases, we are indifferent to the nationality of the companies involved... I listen to all without prejudice or preference," she said.
US companies are often involved in cases because Silicon Valley's dominance in the IT sector, she said, but European companies were fined more often that their American counterparts.
Between 2010 and 2014, 190 European companies were fined $5.1 billion, compared to 17 US companies that faced fines of $698 million.
"It is inevitable that cases involving Google -– in Europe or in the States -– attract the attention of the media, but I will not allow this to become a distraction," she said.