Shaun Williams is set for a spell on the sidelines after suffering a back injury.
The midfielder had to be substituted during Monday night’s defeat to Charlton following a collision with team-mate Clark Robertson.
He left Fratton Park in a wheelchair after the match and was taken to hospital for further assessment.
But Cowley is not yet sure whether the issue will spell the end of the season for the 35-year-old Irishman.
The Blues boss said: “Shaun took a really heavy collision during the game and spent some of the night in hospital before being let out in the early hours.
"We’ll be getting a further scan and then we’ll learn more, but we obviously send him our very best wishes."
“He was in a pretty bad way after the game and had some painkillers injected, but I don’t think he’s getting much sleep.
“Shaun had a scan on Wednesday and, unfortunately, there’s a fracture in his L4 vertebrae, although it does look fairly stable.
“There was still a lot of swelling in the area when he had the MRI, so we haven’t got a totally clear picture yet.
“So we’ll be getting a further scan and then we’ll learn more, but we obviously send him our very best wishes.
“He will be a miss for us in the immediate future, but it’s currently too early to say how long he’ll be out for.”