Phil Jones and Chris Smalling, the England center backs, are out with foot and knee injuries, both suffered on global duty last month.
The young forward has scored three in his last three appearances, including a goal against Chelsea last weekend, and he is finally displaying the abundance of talent he has as a forward under Mourinho.
"I don't think they are easy injuries, but I prefer to wait for all the tests to be done tomorrow", he said.
United issued a statement concerning disaster on Friday morning, tweeting: "Our thoughts go out to the United fans, their friends and families affected by the tragedy in Calabar, Nigeria, yesterday".
Henrikh Mkhitaryan again opened the scoring for United, as he did in Belgium, but his goal was cancelled out by Sofiane Hanni.
United are into the Europa League semi-finals after Marcus Rashford sealed victory over Anderlecht in extra-time of a match which saw both Marcos Rojo and top scorer Ibrahimovic forced off with injuries.
Mourinho, who earlier this season made an apparent criticism of Smalling's pain threshold, said: "We have Daley Blind, who has experience in the position, and I think it is time for Jones and Smalling to be fearless - to risk".
"We are in trouble", Mourinho said.
"Even if he's not in the best condition, if he's not in the level of sharpness that you need to play high-level football".
"I just feel that when a player reaches a certain level, it doesn't make a lot of sense to drop levels", he said.
Manchester United switch their focus back to the Premier League as they travel to Burnley on Sunday (14:15 BST) before travelling to Manchester City on 27 April (20:00). "That is the way we think", Mourinho added. But with a special spirit, it can be sooner than expected.