The 28-year-old was forced to pull out of her second round match in the WTA Rogers Cup in Toronto on Tuesday with a stomach muscle injury.
Clijsters, who had been leading 6-3, 1-2 against China's Zheng Jie before she retired, now faces a race against time to be fit for the US Open.
"I still have a few weeks till [the US Open] and we'll try to do everything to be ready," said Clijsters. "During the match it just felt like it went worse.
"I already had an ultrasound here on site and I have a partial tear in my left stomach muscle and a little bit of blood."
The injury is the latest in a succession of problems for the Belgian, who was forced to pull out of Wimbledon as well as tournaments in Rome and Madrid earlier this year.
The US Open gets underway at Flushing Meadows on Monday, August 29.