Team manager Dusty Baker said Altuve "felt something in his oblique" and was being held from the lineup as a precaution. Baker said this happened during an awkward swing the previous night.
"We certainly can't lose him," Baker said. "Like I told everybody, he's still in Spring Training mode. His mind's not, but his body is. We'll probably rest him today and tomorrow, and then we'll re-assess him."
This comes less than a month after Altuve returned to the team from a previous injury.
The star second baseman had been out of action since March when he was hit by a pitch in the World Baseball Classic while playing for Venezuela against the U.S. He suffered a fractured thumb and required surgery.
Altuve had just made his return to the Astros on May 19.