The former world number one injured sesamoid bones in her left big toe on her way to a 6-4 6-2 win over Estonia's Maret Ani and now faces a six-week lay-off. Roland Garros starts on May 23.
"Roland-Garros? Kim might be fit in time (to play) but we won't be taking any risks," said physiotherapist Sam Verslegers.
"We'll be working to return a step at a time so right now it's difficult to put a timeline on when she will return to action."
Clijsters recently made a sensational return to tennis after having retired in 2007 at the age of 23.
She won the US Open in August 2009 while this year she has added titles in Brisbane and Miami.