"Of course," he replied when asked if Shaw's injury record had influenced his decisions to exclude him from recent squads. "You try to have in the squad the players with more minutes, the players in better shape, in better condition.
"In Luke Shaw's case, even in the game against Reading, when he could have started the game and had 90 minutes, in the morning of the game he was ill and not ready to play.
"So even in that match, which could have been good for him, he was not able to play, so he's having a difficult period."
Shaw's fitness has been under scrutiny since Louis van Gaal questioned it during United's pre-season tour in 2014.
Shaw and Mourinho had a tetchy exchange with Mourinho after Watford's winner in September was followed by another public rebuke at Swansea in November, when Mourinho questioned Shaw's decision to make himself unavailable for the match.
"For the team, you have to do anything," Mourinho said. "There is a difference between the brave, who want to play at any cost, and the ones for whom a little pain can make a difference.
"If I were to speak with the many great football people of this team, they will say they played many times without being 100 per cent.
"We have players on the pitch with problems. In every sport, how many times do you play and you're not 100 per cent?"
Shaw has played just twice since and has sustained five separate injuries this season, while illness prevented him from playing in the September Europa League win over Zorya Luhansk.
Mourinho has rotated between Matteo Darmian and Daley Blind in Shaw's absence. United will not re-sign left-back Patrice Evra from Juventus.
If his career was over he would have been sold in this window. If Jones who has been injured for 80% of his life can turn it around, I'm sure Shaw can too.