Duffy sustained the injury in training and required an operation to remove a blood clot in his leg.
The procedure went well but the 28-year-old will miss Saturday's crunch clash at West Ham and will aim to be available for selection for Watford.
Potter said, “It was just a collision injury on his shin. A hematoma so he just needed to clear that up. We are hopeful he will be available next week."
Solly March is fit having made his return after a groin operation as a second half substitute at Bournemouth. Dan Burn remains sidelined with a shoulder injury and long-term absentee José Izquierdo (knee) is out.
Defender Gaetan Bong didn't train with Albion today and was thought to at Nottingham Forest finalising his move to the Championship club.
Potter was also reluctant to discuss Brighton's link with Chelsea academy graduate Tariq Lamptey. Albion reportedly made a £6million approach for the 19-year-old defender who's contract expires at the end of the season.
"I am aware of him," said Potter. "But I will not comment on a player that is not a Brighton player."