Wales said he was "glad" that Zuckerberg was putting pressure on the Obama administration to stop its "unconstitutional" spying techniques.
"The government...should be here to empower us and to protect our rights...but in fact, the recent revelations have shown a government that's completely out of control, lying to Congress, doing things that are blatantly unconstitutional," Wales told CNBC in a TV interview.
"I think it's a huge scandal."
(Read more: Facebook's Zuckerberg says US spying hurt users' trust )
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.
(Read more: US, tech companies reach deal on spying data )
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.
Secret documents published on news website The Intercept on Wednesday showed that the NSA impersonated Facebook web pages in order to gather information from targets. When those people thought they were logging into Facebook, they were actually communicating with the NSA. The agency then used malicious code on the fake page to break into the targets' computers and remove data from them.
(Read more: NSA likelyoften poses as other sites, say experts )
Last year, Facebook moved to encrypt all its pages, making such impersonation more difficult.
Previous media reports based on leaked Snowden documents detail how the government may have tapped into communications cables that link data centers owned by Google and Yahoo, intercepting user data without the companies' knowledge or cooperation.
"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," Zuckerberg said in his post.
- Reuters contributed to this report