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 told BT Sport.
"But the news is fairly negative I think."
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.
That feeling when you send your club into the #UEL semi-finals! pic.twitter.com/dorfhqLt1h
— Manchester United (@ManUtd) April 20, 2017
"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."