The comments follow a phone call between Zuckerberg and Obama in which the Facebook founder expressed his frustration at the U.S. surveillance program.
For months, a series of revelations leaked by the former National Security Agency contractor Edward Snowden have exposed widespread surveillance through acts such as phone tapping political leaders, and plans to acquire citizens' data via game apps.
"When our engineers work tirelessly to improve security, we imagine we're protecting you against criminals, not our own government," Zuckerberg said in a post on his personal Facebook page.
"I've called President Obama to express my frustration over the damage the government is creating for all of our future. Unfortunately, it seems like it will take a very long time for true full reform," the 29-year-old Zuckerberg continued.
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The White House official confirmed to Reuters that Zuckerberg had spoken to the U.S. President.
But the official declined further comment and referred to the National Security Agency's statement released earlier on Thursday that said recent media reports that alleged the NSA has infected millions of computers around the world with malware and that the agency is impersonating U.S. social media or other websites are inaccurate.
Facebook declined to comment beyond Zuckerberg's post.