Jose Mourinho fears the worst after Zlatan Ibrahimovic and Marcos Rojo were forced off with injuries against Anderlecht.
United were made to sweat after Henrikh Mkhitaryan's early strike was cancelled out by an equaliser by Sofiane Hanni.
The tie was eventually settled in extra-time by man-of-the-match Marcus Rashford as a breathless Europa League quarter-final second leg ended 2-1 at Old Trafford, seeing Mourinho's men through 3-2 on aggregate.
But victory came at a cost as increasingly important defender Rojo left the field on a stretcher in the first half before top scorer Ibrahimovic's knee buckled after landing awkwardly just before extra-time.
Asked about the condition of the pair, Mourinho said: "I want to wait but my feeling is not good for both. I want to wait and try to be optimistic but I am not."
Ibrahimovic was able to hobble off after the injury and Rojo told reporters he was "okay" while limping heavily through the post-match mixed zone.
The Argentina international, so impressive this term, is another blow to a defence already without Phil Jones and Chris Smalling.
Mourinho last week said the England centre-backs were out until mid-May but suggested after the Anderlecht win that they need to be "brave".
"We have Daley Blind, who has experience in the position, and I think it is time for Jones and Smalling to be brave - to risk," said the United boss, who seemed to criticise Smalling's pain threshold earlier in the season.
"Because for the team you have to do everything, that is the way I think. You cannot do miracles, so miracles I don't expect, but they have to try to do everything to accelerate the process.
"They have injuries, and even with a crazy mentality, they cannot play Sunday (at Burnley in the Premier League).
"But with a special spirit, you can (come back) sooner than expected. So instead of mid-May, it could be the beginning of May, this kind of acceleration of the process."