The former Republic of Ireland international was left out of Saturday's 1-1 draw at West Brom after enduing a torrid time against Fulham the previous week.
Two glaring errors in that contest saw the Trotters slip to a 3-1 defeat at the Reebok Stadium.
Megson decided that the centre-half should take a short rest from playing duties in order to put those mistakes to the back of his mind and concentrate on helping the club beat the drop.
"I gave Andy the week off just to clear his head and take a break mentally," Megson told The Bolton News.
"He's a great lad who pushes himself to the absolute limit and it will be beneficial for him just to get away.
"Andy was one of our most consistent players last season and played a major part in keeping the club in the Premier League.
"But I'm sure he'll be back stronger and hopefully the break will work for both him and ourselves."