Zuckerberg was responding to the latest leak by former NSA contractor Edward Snowden, detailing an NSA program that imitates a Facebook server in order to access a user's computer files.
Zuckerburg said that he has been disappointed by the government's surveillance activities.
"The internet works because most people and companies do the same. We work together to create this secure environment and make our shared space even better for the world," he wrote. "This is why I've been so confused and frustrated by the repeated reports of the behavior of the US government. When our engineers work tirelessly to improve security, we imagine we're protecting you against criminals, not our own government."
The White House confirmed to Time Magazine that Obama spoke with Zuckerberg.