The Irishman tonight left Fratton Park in a wheelchair having sustained a blow to his back in the second half of the match.
Although able to leave the field on his feet following a penalty-area collision, Williams later had to be attached to a drip and was given painkillers.
Following the game, medical staff wheeled him along the touchline on their way to QA Hospital for assessment.
And Cowley, who stopped post-match interviews to wish the midfielder well, spoke of his concern for his player.
He told The News: ‘Shaun got a really bad, heavy bang to the middle of his back.
‘It just seized up, we don’t quite know what the extent of it is yet.
‘It was a collision, three of them jumped together and he has hurt his back.
‘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.’
Williams left the field in the 71st minute to be replaced by Louis Thompson in the centre of midfield.
He had initially collided with team-mate Clark Robertson and a Charlton player, requiring medical treatment on the pitch.
Williams has made 30 appearances for Pompey this season after arriving from Millwall on a free transfer in the summer.
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