Daily Tagesspiegel reported on Wednesday that the 30-year-old man lost control of his jump, ricocheted off the sixth floor of the opposite building and smashed into a telephone box before hitting the ground.
He was taken to hospital with life-threatening injuries, police told the paper.
A security guard for the site found a 32-year-old man, believed to be the injured man's friend, crouching over the base-jumper on the footpath next to the Zoofenster construction site, which will house the new Waldorf-Astoria hotel.
Tagesspiegel reported that the jumper had a serious fracture to his femur as well as severe internal injuries.
Police are still investigating what caused the base-jumper to lose control during the descent. They are examining footage taken by a camera attached to the man's helmet which was intended to film the drop, a common practice among base-jumpers.
His suspected companion had initially hidden the camera following the accident.
“It's like you were there,” a police spokesperson said of the camera recording, which he said clearly showed how the man was able to enter and scale the building.
The man jumped from scaffolding surrounding the roof of the 118 metre-tall Waldorf Astoria luxury hotel on Hardenbergplatz in Berlin's Charlottenburg district at 3.35 am.
The security guard stated that he clearly heard the base-jumper's parachute open during the fall.
Base-jumping is the practice of jumping from large, fixed objects such as high-rise buildings or even windmills.
The man is being investigated for trespassing, as the practice is illegal in all German inner-cities, although occasional permission is granted for events.
The Verein Deutsche Objektspringer (German Basejumping Association) has been lobbying to gain official recognition of base-jumping as a sport, which would allow base-jumping sites to be more thoroughly evaluated for safety.