The officials said on Monday there were "serious shortcomings" in the report made public in July.
In a letter sent to Congress, they called on legislators to "apply brakes to the race to implement the commission recommendations".
The letter was signed by 25 officials who formerly worked in the CIA, FBI, US Customs, Department of Homeland Security, the Federal Aviation Administration and the US military.
The report "deliberately ignores officials and civil servants who were, and still are, clearly negligent and/or derelict in their duties to the nation", they said.
"If these individuals are protected rather than held accountable, the mindset that enabled September 11 will persist, no matter how many layers of bureaucracy are added, and no matter how much money is poured into agencies," the group added.
Retired senior CIA analyst Melvin Goodman, one of the signatories, blasted the commission's recommendation to create an "intelligence tsar" to centralise US intelligence efforts.
"I cannot think of a better way to politicise intelligence than to appoint an intelligence tsar," he said.
The shortcomings of US security and intelligence were known well ahead of the September 11 attacks, Goodman said, and those responsible for not fixing the problems had to be held accountable.
New York's JFK airport has been
cited for its security loopholes
"People in the American government helped create this tragedy. Until we understand this the chances of another September 11 remains," he said.
Bogdan Dzakovic, who formerly led a mock terrorist squad known as Red Team for the FAA, said he had been pointing out security shortcomings for years before the September 11 attacks, to no avail.
"The US faces the biggest threat since the end of the Cold War, but it is from the government's own bureaucracy," he said.
Another signatory, Diane Kleiman, a former US Customs agent who worked at New York's John F Kennedy International Airport, said while passengers are checked heavily, cargo handlers, maintenance and clean-up crews have easy access to the planes.
There is a high turnover rate among cargo handlers, she said, and security is extremely lax when it comes to keeping track of magnetic cards that allow access to back doors that open to the runway.
As proof she produced her own security clearance pass, which was never collected by airport authorities, although she was fired in 1999.