"The artists aren't very happy about this, but in the end their paintings and their art will not disappear, it will just not be in the wall but behind it," he told The Associated Press.
Another small section of the East Side Gallery was removed a few years ago in conjunction with the building of a new sports and concert arena.
Thoms said the road will give pedestrians access to a new footbridge across the Spree that was destroyed during World War II and is being rebuilt by the city, as well as another condo project.
The East Side Gallery was transformed into an open-air gallery months after East Germany opened its borders on Nov. 9, 1989, and is now covered in colorful murals painted by about 120 artists. They include the famous image of boxy East German Trabant car that appears to burst through the wall; and a fraternal communist kiss between Soviet leader Leonid Brezhnev and his East German counterpart, Erich Honecker.
Crews were only able to remove one approximately 1.5 meter (yard) section on Friday from a mural depicting a stylized version of another Berlin landmark, the Brandenburg Gate, before the protests stopped the work.
Robert Muschinski, one of the protest organizers, called the demonstrators' success a "historic moment."
"It's a scandal and it's embarrassing," he said. "Today we showed the world we would destroy a longtime part of our history in favor of the interests of private investors."
Ciaran Fahey and Kerstin Sopke contributed to this story.