Philadelphia general manager Paul Holmgren said in a statement Wednesday that both players hurt their right foot during Tuesday night's game. They are listed as day-to-day.
Carter led the team in goals with 33 during the regular season, and has two goals and an assist in the playoffs. He missed eight games toward the end of the regular season with a fractured left foot.
He was injured by a shot from teammate Chris Pronger while scoring his second goal of the game in the third period of the Flyers' 4-1 win in Game 4.
The Flyers were awaiting results of a CT scan taken on Carter's foot early Wednesday.
Gagne has two assists in four playoff games, helping the Flyers take a 3-1 lead in the best-of-seven Eastern Conference series. He was hurt on Ilya Kovalchuk's shot with 4:30 to play in the second period.
"It's tough. It seems like I just got off" crutches for the other foot, Carter said. "It's definitely disappointing. I really felt like I was getting back into my groove and get some jump in my game. Another setback like this, it's tough."
The Flyers indicated that Ville Leino, acquired from Detroit this season, will fill one of the vacancies. General manager Paul Holmgren indicated the second vacancy will be filled by either David Laliberte, Andreas Nodl or Jon Kalinski, all recent call-ups from the Adirondack Phantoms.
"Everybody deals with that in the playoffs," coach Peter Laviolette said. "You wish you had a healthy lineup and you certainly wish they were in there. They are not and you have to make adjustments."