"I've called President Obama to express my frustration over the damage the government is creating for all of our future," Zuckerberg said in a post. "Unfortunately, it seems like it will take a very long time for true full reform."
Zuckerberg's post comes a few days after a report that alleged the National Security Agency has previously posed as Facebook so that it could infect users' computers with malware. The NSA has called these claims false.
In his post, the Facebook co-founder said his company has worked for years to create a secure environment, but never did he imagine that protection was needed from the government.
"I've been so confused and frustrated by the repeated reports of the behavior of the US government," he said. "When our engineers work tirelessly to improve security, we imagine we're protecting you against criminals, not our own government."
Zuckerberg said Facebook is committed to keeping users and their information secure, but he advised the government to be more transparent about its activities.
"Otherwise people will believe the worst," he said.