The 26-year-old underwent an operation on shin splints in March but recovered well enough to make four appearances for City's first team earlier in the season.
But the former Cheltenham man suffered a break to his left shin during a reserve game against Bournemouth on Tuesday, with his recovery time yet to be determined.
Johnson told the club's official website: "Everyone's gutted for him and it's been a difficult few weeks.
"He suffered a bereavement in the family and now this has happened after only a couple of minutes playing for the reserves.
"The first scan showed up a fracture on his shin bone but we're going to get a second scan just to make sure. We need to help him because it's been a tough time for him."