The Blues striker returned to action against Huddersfield Town on Saturday after 10 weeks out with a thigh strain.
However he is now struggling with a shoulder problem and could miss out on facing Hartlepool.
Speaking to the Southend Evening Echo Blues boss Steve Tilson said: "Dougie picked up the injury at the weekend when he was fouled on the edge of the box and we're not sure if he will be able to play. It's unbelievable really and of course it will be a blow if he doesn't play. Dougie's a quality player and he made a difference when he came on against Huddersfield. It gave us a lift having him back so to be missing him again would be very disappointing indeed."
Freedman has yet to train this week and a decision on his fitness will be made today before Blues fly to the north-east.
The 34-year-old joined the Shrimpers on a free transfer from Championship club Crystal Palace at the start of September but he has made only five appearances since scoring four goals.
This is starting to become a bit of a farce, Barny slipping on the tarmac while catching the plane anyone?
Dougie playing a full 90 minutes was a real source of hope after the last few weeks, let's hope we'll see it happen again soon.