Wanderers have no plans to hand over the entire South Stand at the Reebok to visiting fans.
Flare-ups at the recent Premiership clash with Everton were caused when visitors, who missed out on the 3,000 ticket allocation for the away section of the ground, infiltrated home areas.
But commercial director, Gareth Moores, says Wanderers are determined to keep a section of the South Stand for home supporters.
"The Everton game was all but a sell-out," he said, reflecting on the record attendance of 27,383, "and if we had offered 5,000 seats to visiting supporters, there would have been 1,500 or more of our own supporters who would not have seen the game.
"We are seeing attendances grow and we want to provide as much opportunity as possible for our own supporters to see the games. Hopefully, as the season progresses, we will see more and more games attracting capacity crowds.
"Unfortunately, when the away team sells its allocation of tickets, it presents problems but we do everything we can to make sure visitors don't get into the home sections.
"It causes problems but we are reluctant to provide additional seating to visiting supporters."
Wanderers have investigated scores of complaints about disturbances at the Everton game but say they are taking every possible measure to ensure the safety of supporters.
"Yes, we had away fans in home areas," Mr Moores acknowledged, "but the club tries very, very hard to ensure that doesn't happen. Unfortunately, there are Everton people who live in this part of the world, just as there are Bolton supporters who live on Merseyside.
"We have an obligation to do everything we can to prevent away supporters sitting in home sections but, unfortunately, we have heard of Bolton supporters giving tickets to Everton supporters.
"It's a sad indictment of football that we have to have segregation but that is the reality.
"We have to put this into perspective though. This problem is not unique to Bolton Wanderers and this is a very safe and family friendly place to come to watch football. Unfortunately, on very rare occasions - and Everton was one - we have a problem which needs to be dealt with."
Comments: Our rules
We want our comments to be a lively and valuable part of our community - a place where readers can debate and engage with the most important local issues. The ability to comment on our stories is a privilege, not a right, however, and that privilege may be withdrawn if it is abused or misused.
Please report any comments that break our rules.
Read the rules hereComments are closed on this article