The suspects, spread across 40 states, are thought to be engaged in "low-level support activities" such as raising money, relaying messages and recruiting members, according to a report in Saturday's New York Times.
Investigators do not see evidence that a fresh attack is imminent but are alarmed by a widening presence of al-Qaida sympathisers on US soil.
"Every month, we continue to identify new people aligned with al-Qaida in the United States," said a senior US official who declined to be identified.
"It's an ongoing process but it is disconcerting that every month, almost every week, we find additional people here who are sympathetic to al-Qaida and its goals."
Officials can now obtain and execute a search warrant without notifying a suspect beforehand.
In a strategic shift, authorities are closely monitoring the suspect groups and individuals rather than detaining them.
"By taking down a group too early, you may be losing a lot of opportunity for valuable intelligence," explained another US official. "Who are their associates? Who else is out there that we don't know of that these individuals may contact?"
The detection of al-Qaida followers has been accelerated by controversial new law enforcement standards that critics say are degrading civil rights in the United States.
The changes, many of them contained in the USA Patriot Act, were instituted after the September 11, 2001 terror attacks in New York and Washington that killed 3000.
For example, officials can now open a criminal inquiry based only on a "reasonable suspicion" of suspect activity, and they can obtain and execute a search warrant without notifying a suspect beforehand.