In a post on his own Facebook page, the founder of the huge social network expressed anger towards Washington, in what appeared to be a reaction to new revelations about US government surveillance.
"I've called President Obama to express my frustration over the damage the government is creating for all of our future," he wrote.
"Unfortunately, it seems like it will take a very long time for true full reform."
Zuckerberg's comments come amid growing tensions between the tech sector and US administration over leaked documents describing the vast surveillance ability of the secretive National Security Agency and other intelligence services.
"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 said.
"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."
He added: "The US government should be the champion for the Internet, not a threat. They need to be much more transparent about what they're doing, or otherwise people will believe the worst."
The comments came a day after a report citing leaked NSA documents said the spy agency had imitated a Facebook server to inject malware into computers to expand its intelligence collection capacity.
The report by former Guardian reporter Glenn Greenwald said the NSA had developed malware that allows it to collect data automatically from millions of computers worldwide.
Some of the documents leaked by former intelligence contractor Edward Snowden in recent months have said the NSA had access to servers of tech giants such as Facebook, Google and Yahoo.
These companies have strongly denied giving any access except under a legal requirement, and have said more transparency about the programs could reassure their customers.
An agreement in January allowed the companies to publish broad details of government data requests, but many activists have called for far more information.
Zuckerberg, in his posting Thursday, reiterated his call for more openness.
"As the world becomes more complex and governments everywhere struggle, trust in the Internet is more important today than ever," he said.
"To keep the Internet strong, we need to keep it secure. That's why at Facebook we spend a lot of our energy making our services and the whole Internet safer and more secure.
"We encrypt communications, we use secure protocols for traffic, we encourage people to use multiple factors for authentication and we go out of our way to help fix issues we find in other people's services."
Zuckerberg's comments drew a quick response online, with 73,000 people hitting the "like" button within an hour and more than 8,000 "shares."
Dozens of people commented on Facebook, mostly to praise Zuckerberg.
"Thank you Mark! It's good to know that you do have us in mind first!" one Facebook member wrote. But another warned: "I hope this is sincere and not like Google's 'don't be evil' two-faced mantra."