Coach Andy Reid said Samuel, who did not practice in the afternoon, will probably have an MRI on Sunday.
"He felt a little better once he got in [after practice]," Reid said following the afternoon session.
The All Pro signed a six-year, $57 million contract with the Eagles after spending his first five seasons with the New England Patriots. He missed time during the team's workouts last month with a strained left hamstring.
If Samuel is out for an extended period, the Eagles have depth at the position. Two-time Pro Bowl cornerback Lito Sheppard, who lost his left cornerback spot to Samuel and wanted a trade, would step in.