Manager Andy Hessenthaler told BBC Radio Kent: "It looks like a medial ligament injury to the knee, and that could be a bit of time."
"We've also lost Dennis Oli (winger) with a torn hamstring, and striker Cody McDonald is struggling." he said.
Oli could be out for between four and six weeks.
Gillingham are also without defender Simon King, who has an ankle injury which means he is unlikely to play before Christmas, while centre-half Gary Richards and striker Mark McCammon have not played a game in pre-season.
Hessenthaler said: "It is a concern because at this stage we do not want to be picking up injuries.
"Barry went in for a good challenge and it's opened his knee up. He will be a loss and since I have taken over at the club he has been fantastic, he has been a proper captain.
"We'll have to see how long and how bad it is."
Source: BBC Sport
Source: BBC Sport