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The U’s saw Jay Williams suffer an ankle injury during their FA Cup victory over Worcester City, with the midfielder eventually forced off on the hour.
Williams had initially sustained the problem in the first half of the U’s 1-0 win and, despite attempting to play through it, was unable to continue.
The 25-year-old is due to join up with St Kitts and Nevis for international duty, this week.
Cowley said: “Jay hurt his ankle. He did it in the first half.
“It was really swollen at half-time.
“He’s tough, so he went out and got on with it but he just deteriorated.”
Williams is the latest addition to a lengthy injury list which has caused significant disruption for the U’s.
Rob Hunt missed the Worcester victory after suffering a groin problem at the start of the week, while fellow defender Frankie Terry injured his knee in an unusual training-ground accident.
Sidelined - Colchester United defender Rob Hunt has suffered a groin injury (Image: Richard Blaxall)
Goalkeeper Tom Smith is another late casualty after hurting his shoulder on the eve of the Worcester game.
Cowley said: “We lost Hunty on Monday and Frankie on Thursday.
“Hunty’s groin just tightened up, so we don’t think it’s too bad.
“Frankie stepped down a sprinkler and hyperextended his knee.
“You have these pop-up sprinklers. We’re lucky to have them but sometimes you have these challenges.
“Tom Smith landed awkwardly on his shoulder [on Friday] and missed out.”
Colchester had hoped Teddy Bishop and Beryly Lubala would be available after both trained during the week, but neither was considered ready to return for the Worcester game.
“Teddy and Bez trained all week but when push came to shove, weren’t quite happy unfortunately,” said Cowley.
Out - Colchester United striker Kylian Kouassi is sidelined with a hamstring injury (Image: Richard Blaxall)
The fresh setbacks come with Leon Chiwome, Kylian Kouassi, Harry Anderson and Jake Leake already sidelined through injury.
And the sheer number of fitness problems is now having an impact on the way Cowley and his team are able to prepare the squad between matches.
The U’s boss revealed they had deliberately reduced the intensity of training in an effort to prevent further casualties.
“It’s tough,” he said.
“On Thursday, 90 per cent of the work we did was unopposed because we keep picking up so many injuries.
“We’re trying to pick the bones out of it, because all of our success in our careers has come from getting your best players on the pitch as often as you can, so we’re just trying to understand it really.”