The world number eight's announcement follows the decision by Wimbledon runner-up Milos Raonic and Simona Halep to withdraw from next month's Rio tournament.
"It was a hard decision for me to take after a long and painstaking discussion with my dearest," Berdych, 30, said on his Twitter page on Saturday.
"It is because of the Zika virus spread in the country of the Olympics. As I have founded a family recently, to limit health risks towards my nearest is the utmost priority."
Several top golfers have opted to skip the Olympics because of concerns about the mosquito-borne disease which is linked to birth defects in newborn babies.
"I apologise to all of you who are disappointed by my decision. I do believe that if you take a deeper account of my reasons you will understand that I have done it out of the responsibility for my family," Berdych added.
The Czechs still have Jiri Vesely and Lukas Rosol on their Olympic team.
Raonic and women's world number five Halep withdrew on Friday. They, along with twice Australian Open champion Victoria Azarenka, who is pregnant, will not be making the trip to Rio even though they were included in the final list of participants issued by the International Tennis Federation (ITF) on Friday.
(Reporting by Martyn Herman, editing by Pritha Sarkar)
