The Facebook boss was "virtually" transported to Puerto Rico with Rachel Franklin, the head of social VR at the company.
In the video on his Facebook page, Zuckerberg said: "One of the things that's really magical about virtual reality, is you can get the feeling that you're really in a place."
Franklin followed up and said: "Crazy to feel like you're in the middle of it."
The comments and the entire video were repeatedly slammed by users on social media.
One user on Facebook, Rosaida Castro, commented on the video on Zuckerberg's page and said: "Is this a joke? The Puerto Ricans are suffering and you are using our tragedy for this?? Heartless billionaire."
Other users said Zuckerberg was engaging in "voyeuristic tourism."
Another user Paul Rickett said Zuckerberg "can't let a good tragedy go to waste. He has to promote Facebook. Typical. All he talks about (is) Facebook instead of victims and their suffering."
In a comment on his post, Zuckerberg wrote: "One of the most powerful features of VR is empathy. My goal here was to show how VR can raise awareness and help us see what's happening in different parts of the world. I also wanted to share the news of our partnership with the Red Cross to help with the recovery. Reading some of the comments, I realize this wasn't clear, and I'm sorry to anyone this offended."
Zuckerberg's reaction to the disaster stands in contrast to that of another high-profile tech innovator, Elon Musk. The CEO of Tesla last week proposed rebuilding Puerto Rico's electricity infrastructure using solar systems.
Some people who watched Zuckerberg's video praised his efforts in VR, as well as Facebook's assistance to those affected by Hurricane Maria.
The Facebook CEO talked about features like Safety Check, which allows users on the social network to mark themselves safe when a natural disaster hits. He also said the company had donated over $1.5 million to the relief efforts in Puerto Rico.
Zuckerberg also said the company is using artificial intelligence to map the population in Puerto Rico to help the Red Cross identify areas most in need of help.