The 29-year-old said in a blog post the US government "should be the champion for the internet, not a threat".
His comments come a day after a report the US National Security Agency (NSA) imitated a Facebook server to infect surveillance targets' computers.
The NSA said the report was "inaccurate".
Mr Zuckerberg said in September that the US "blew it" on internet spying.
The tech founder wrote on Thursday "it seems like it will take a very long time for true full reform".Broken trust?
"When our engineers work tirelessly to improve security, we imagine we're protecting you against criminals, not our own government," he said in his blog post.Continue reading the main story How intelligence is gathered Accessing internet company data 'Tapping' fibre optic cables Eavesdropping on phones Targeted spying Read more in our in-depth report How the US spy scandal unravelled Profile: Edward Snowden
"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 NSA's activities were leaked by a former contractor for the agency, Edward Snowden, last year.
His leaks have pointed to the NSA collecting phone records, tapping fibre-optic cables that carry global communications and hacking networks.
According to the documents, the agencies had "backdoor" access to the servers of nine major technology companies including Microsoft, Yahoo, Google, Facebook, PalTalk, AOL, Skype, YouTube and Apple.
All the companies named have denied their involvement.
The NSA called the latest claims, that it expanded surveillance by using malware, "inaccurate".
The agency said in a statement: "The NSA uses its technical capabilities only to support lawful and appropriate foreign intelligence operations, all of which must be carried out in strict accordance with its authorities."
White House spokeswoman Caitlin Hayden confirmed that the president spoke with Mr Zuckerberg on Wednesday evening regarding "recent reports in the press about alleged activities by the US intelligence community.'' She gave no further comment.'Setting fire'
Since claims emerged that the security services were using social media and technology companies to monitor people, Facebook has teamed up with Google, Apple, Microsoft, Twitter, AOL, LinkedIn and Yahoo to form an alliance called Reform Government Surveillance.
The group has called for "wide-scale changes" to US government snooping.
In his latest blog post, Mr Zuckerberg said that to keep the internet strong, "we need to keep it secure".
Earlier this week, Mr Snowden told a conference that mass surveillance conducted by the US and other governments was "setting fire to the future of the internet".
Earlier this month, European Commission Vice-President Neelie Kroes said billions of people around the world do not trust the internet.