Club captain Puyol had arthroscopic surgery on the cartilage in his right knee in March and Mascherano damaged ligaments in the same joint in Barca's 2-2 quarter-final first leg draw at Paris Saint-Germain on April 2.
"Puyol won't be available for the game in Munich and we don't know yet about the return leg [on May 1], it will depend on how he recovers and the doctor's decision," Roura, standing in for coach Tito Vilanova while he recovers from cancer treatment, told a news conference.
"Mascherano is coming along well but we still don't know whether he can play in the return leg," he added.
"We have to take it step by step," Roura said of the Frenchman.
"It's normal that he is keen to play, just like his team-mates.
"He has worked extremely hard and he is more ambitious all the time."
One player who appears certain to have recovered from injury before Tuesday is Barca's Argentina forward Lionel Messi.
"Messi is in good shape," Roura said. "He is back working with the group again and he has coped well with his recovery and is doing all he can to be fit."
