The 30-year-old former Norwich, Celtic and Scunthorpe forward sustained a hip injury in December and has been sidelined for the past nine months.
The Sky Bet Championship club are now seeking a second opinion after Hooper reported he was still in pain following a 60-minute appearance for the Owls' under-23 team last week.
Hooper, who began his career as a Tottenham youth player before going on to make 69 appearances for Grays, has been ruled out of training with the senior side while his latest injury is checked out.
Wednesday manager Jos Luhukay confirmed the player would be sent for tests and a second opinion due to the length of the injury and lack of progress.
Luhukay told the club's official website: 'Gary Hooper has not trained fully with the team this week so he must go to a second opinion to another doctor because he still has pain.
'It's frustrating but we must live with the situation that it will take time to come back to 100 per cent in the team training. It's frustrating and disappointing for him.'
Hooper moved to Hillsborough permanently in January 2016 following a successful loan spell from the Canaries earlier that same season and has scored 30 goals in 83 appearances - in all competitions - for Wednesday since making his debut.