Scans have revealed the 35-year-old midfielder damaged his L4 vetebrae during the second half the Fratton Park fixture following a collision with team-mate Clark Robertson, whose knee accidentally caught the Irishman in the back.
The former Millwall man will have a further cat scan tomorrow to reveal the true extent of the injury.
According to Blues boss Danny Cowley, it’s too early to say’ whether Williams will miss the rest of the season.
Williams was immediately removed from Monday night’s action on 71 minutes and was seen leaving the ground in a wheelchair as he headed to hospital.
Speaking to The News immediately after the defeat to Charlton, Cowley said: ‘He is in a really bad way, he’s had some painkillers and is obviously going to hospital for a scan.
‘There was a drip in his arm, putting painkillers in as quickly as they could.
‘Shaun was in a bad place, we couldn’t have too much communication with him.’
Pompey currently have Joe Morrell, Louis Thompson and Ryan Tunnicliffe as their midfield options after loanee Miguel Azeez returned to parent club Arsenal during the January transfer window.