The Welshman came off his bike around 30 kilometres from the end of stage four of the race and was treated at the side of the road.
Team Ineos reported the 33-year-old remained conscious.
"Sadly @GeraintThomas86 has been forced to abandon the #TourDeSuisse. He was alert and speaking to the team after the crash and will be taken to hospital for checks. Further updates to follow," read a tweet from Team Ineos.
According to cyclingnews.com, Tour de France champion Thomas suffered cuts to his back and above his right eye.
He is due to lead Ineos at this year's Tour, which takes place next month, after team-mate Chris Froome said he was "lucky to be alive" following a crash last week in France for the Criterium du Dauphine.
Froome underwent extensive surgery following his high-speed crash, which left him with multiple injuries, including a broken femur.