Headley was injured in a rundown drill Saturday morning. A team spokesman says he'll likely undergo an MRI on Monday.
Headley had declared himself fit earlier in the week after minor offseason knee surgery.
Headley led the National League with 115 RBIs in 2012 before his numbers dipped last season. He signed a one-year, $10.5 million contact in January and has said he doubts the two sides can reach an agreement on a long-term deal before the start of the regular season.
It's the first significant injury of spring training for the Padres, who were 76-86 last season.
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