His 'shattered' Robins side played seven times in 21 days and Cotterill pinpointed fatigue as a key factor in allowing Tranmere to twice come from a goal down to earn a 2-2 draw on Saturday.
And the City boss says his players will take some time off to recharge their batteries.
"I think it is important the players get some recovery time," he told the Bristol Evening Post. "They will have a couple of days off, because it is the right thing to do.
"It is not just the seven games in 21 days that have taken a toll, but the state of the pitches and the conditions they have had to play in.
"I think everything has caught up with us and we didn't have that spring in our step which we have had recently. I think beating Orient took a lot out of them and they looked shattered."
- Sports & Recreation