Portsmouth are investigating after a plastic bottle was thrown from the crowd towards Bristol Rovers' Tom Lockyer at Fratton Park.
Rovers captain Lockyer had just received treatment for an injury when the incident happened.
A club spokesperson said Portsmouth were "made aware that a bottle was thrown from the stands" and "are investigating along with the relevant authorities."
The Football Association confirmed on Wednesday that they were looking into the incident.
Meanwhile, Rovers manager Graham Coughlin told BBC Radio Bristol on Thursday that the FA will not be taking any action against Portsmouth striker James Vaughan following allegations he punched Lockyer in the same match.