Wales captain Bellamy has withdrawn from his country's squad ahead of the weekend's friendly with Scotland due to a sore groin and Hughes believes the 30-year-old may have to concentrate only on competitive games in the future.
"As time goes on, there could be that situation," he said. "Craig knows his body better than anybody else and when he feels he needs a break or senses he could have an issue if he continues training or playing, he is quite clued in on that and he will pull himself out of things.
"I think that's how it will be in the future and it will be better for him and them (Wales) because it will enable him to ensure that his career runs its course and is as long as it can be.
"Craig is a bit sore at the moment. We have to protect him and try not to play him in midweek games. We have to protect him because it is a long season and we want to get the best out of him."