Central midfield looked to be the strongest area of the pitch for Pompey back in August.
But a leg fracture sidelined Louis Thompson and injuries to Marlon Pack, Tom Lowery and Joe Morrell have all followed.
It has left the side somewhat depleted, but they still managed to fight from behind to draw with Oxford at Fratton Park on Tuesday evening.
Kyle Joseph fired the visitors in front with a fine strike before they had Billy Bodin sent off, with Colby Bishop slotting home the leveller.
And Cowley was pleased that his depleted side fought against adversity to display their battling qualities.
The Blues boss said: “I’m proud of the group because of what’s gone against us – I think that’s 10 injuries now.
“We went into the game with four key midfielders out and anyone will know that no matter what you do on the training pitch, you’re just not going to be as good.
“At the moment we’re just not staying on the right side of the injury situation and it’s something we have to look at.
"We weren’t perfect by any stretch of the imagination, but have a group with plenty of grit and determination."
“Our squad is stretched and two players made their first league starts on Saturday, then you’re asking them to back it up on the Tuesday.
“It’s difficult and we went too direct in the first half, but credit to Nicky because he wanted to change it.
“When you’re a goal down and you take off a forward to play an extra midfielder, it’s pretty brave. But when we put together five or six passes, we were able to cause Oxford problems.
“I think the red card was through our good play because we got through their press and they had to keep fouling us.
“We weren’t perfect by any stretch of the imagination, but have a group with plenty of grit and determination.
“We’re battered and bruised at the moment, but we’re Portsmouth Football Club and we’re never beaten.”
Cowley will now have to assess the fitness of Sean Raggett and Reeco Hackett, who both had to be replaced.
He said: “I’ve never known Sean to come off – I remember him getting teeth knocked out and having stitches in his head.
“He’s a warrior and the fact he’s needed to be substituted means it will unfortunately be bad, while Reeco also took a nasty whack.”