Two people inside the vehicle died in the incident
One member of staff and a person from a partner company died in the crash.
The incident took place on Wednesday at around 17:20 local time, the firm said. The people that died were inside the vehicle as it fell from the building.
Nio says it immediately started an investigation into the incident in co-operation with government officials.
The third storey area from where the car fell has been variously described as a showroom, a testing facility or a car park.
"Our company has collaborated with public security department to launch the investigation and analysis of the cause of the accident. Based on the analysis of the situation at the scene, we can initially confirm that this was an accident (not caused by the vehicle)," the company said in a statement.
"We feel very sad about this accident and would like to express our deepest condolences to our colleague and partner employee who lost their lives. A team has been set up to help the families," it added.
Nio's initial statement on Weibo attracted more than a thousand comments within half an hour, but was then taken down.
The last sentence of the statement "not related to the vehicle itself" triggered many angry responses from social media users.
One comment read "it shows the cold blood of capitalism," while another said "The last sentence is so indifferent. They [test drivers] came to test the vehicle, but you say [the accident] has nothing to do with the vehicle?"
Yet another Weibo user said "It should be public security bureau to confirm if it's an accident or not."
The carmaker has since posted a revised version of the statement, which still refers to the crash as an accident but now has "not caused by the vehicle" in brackets apparently to de-emphasise that part of the sentence. All the comments to the new post are now "RIP".
Nio is at the forefront of China's home-grown drive to dominate the electric vehicle industry. It has bet big on interchangeable batteries in its cars as a way to overcome customer concerns about frequent charging.
The company has sometimes been called China's "Tesla killer", in a reference to its rivalry with multi-billionaire Elon Musk's US-based electric car maker which has a major manufacturing plant in Shanghai.
One social media user posted a photo, apparently taken from a nearby building, marking with a red circle the window from which the car fell
-- Courtesy of BBC News