The campaign is currently suspended until at least April 30 because of the coronavirus crisis, with the Potters just three points above the relegation zone.
“The difficult thing will be how we manage them back into training,” O’Neill told the club.
“That’s why it’s important that they stay in as good a condition as possible so when we come back in we can train them at the level that we’d like to, so we’re not getting scenarios where players are overloaded and breaking down.
“And if we are asked to play the remaining nine games in a short space of time it’s going to be a real burden on the squad.
“It’s going to apply a lot of pressure and players aren’t going to be able to play with that frequency and not have injuries, common sense tells you that will be the case.
“If you’re playing midweek every week, if that scenario does prevail, we have to make sure the squad is as robust as possible to fulfil those fixtures.”