Ibrahimovic and Rojo suffered knee problems as United edged into the Europa League semi-finals with a 2-1 extra-time win at home to Anderlecht.
But the 3-2 aggregate success came at a price, with Ibrahimovic and Rojo both seemingly set for extended spells on the sideline after being taken off.
"I don't think they are easy injuries but I prefer to wait until all the tests are done and then speak. I can't do that because I am a manager not a doctor," Mourinho said.
"But the news is fairly negative I think."
Veteran striker Ibrahimovic was forced off before extra time after landing awkwardly after challenging Kara for a high ball in the 92nd minute of regulation time and went down for treatment.
Ibrahimovic subsequently hobbled down the tunnel with the assistance of medical staff and was replaced by Anthony Martial for the additional 30 minutes.
It was another blow for United, who had already lost Rojo to a knee injury that resulted in him being taken off on a stretcher in the first half.
Henrikh Mkhitaryan again opened the scoring for United, as he did in Belgium, but his goal was cancelled out by Sofiane Hanni.
It took until the 107th minute for the hosts to secure their win through Marcus Rashford, who had been goalless in the Premier League since September before netting in back-to-back games earlier this month.
"You speak about his qualities and they are fantastic. But mentally he is excellent," Mourinho said.
"He hadn't scored since September, some players don't understand what I want but Marcus I trust.
"It doesn't matter if he doesn't score - he is fantastic in his effort and attitude."