The Facebook founder and another executive discussed the platform's virtual reality project through avatars in a video recorded live Monday.
The video begins with the avatars pictured on the roof of Facebook's Mountain View, California, headquarters before heading to Puerto Rico by using a 360-degree video recorded by National Public Radio as a backdrop.
Zuckerberg later responded to critics, writing that his goal of showing "how VR can raise awareness and help us see what's happening in different parts of the world" wasn't clear.
Facebook is also working to restore internet connectivity on the island and has donated money to the relief effort.