The second seed needed treatment on his long-standing right shoulder injury during his 6-2, 7-6 (7/5), 6-4 win over France's Adrian Mannarino.
But as well as worrying about the state of his shoulder, the 30-year-old slammed the poor quality of the All England Club courts.
"I told the chair umpire that there was a hole in the middle of the court on the service line. I showed him and he was not very pleased about it," said Djokovic.
"I have played on better courts."
Djokovic needed treatment on his right shoulder after the fifth game of the third set and a medical timeout at 4-3 to treat the same problem.
He had already summoned the doctor after just three games of the opening set.
"We'll see on the shoulder. It is something which I have been dragging back and forth for a while but I am still managing to play," he added.
Berdych will have had a day more to rest up for the match as Djokovic and Mannarino were scheduled to have played their last-16 match on Monday.
However, their tie was pushed back to Tuesday after Gilles Muller and Rafael Nadal played out a marathon fourth round match which lasted a shade under five hours.
Djokovic and Mannarino were first up under the Centre Court roof as rain fell on the courts.
"It was a long day yesterday for both of us waiting for an entire day. It is what it is. We got on the court today and we could play under the roof," said Djokovic.
"I haven't dropped a set yet on grass this season either here or in Eastbourne. I have been feeling really good. I am motivated to go as far as I can."
Berdych hasn't defeated Djokovic since 2013 but he did triumph over the Serb at Wimbledon in the semi-finals seven years ago when the Czech finished runner-up to Nadal.
"He beat me here in 2010. He has the big game, big serve and forehand and hits the ball very flat.
"He's an established top-10 player. He knows and understands the big matches.
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