The massive FBI probe that triggered raids in Queens is focused on a Denver-based terror cell plotting another attack on the scale of 9/11, the Daily News learned Tuesday.

Hundreds of FBI agents are on the ground in Colorado, conducting round-the-clock surveillance on five suspects – including a man who recently visited Queens, sources told The News.

New York authorities searched three Flushing apartments and detained several men – later released – after getting a warrant to look for bomb-making components, explosive powders and fuses.

“The FBI is seriously spooked about these guys planning another 9/11,” a former senior counterterrorism official told the News. “This is not some … FBI informant-driven case. This is the real thing.”

Police Commissioner Raymond Kelly told reporters it’s an ongoing investigation with plenty of “substance.”

The 24-7 counterterror operation included Foreign Intelligence Surveillance Act warrants used to intercept calls and e-mails, as well as overseas-linked wiretaps to eavesdrop on Arabic and Pashto-speaking targets.

Sources said the investigation’s targets are Afghans – an unusual development. Al Qaeda prefers Arabs and Pakistanis as there overseas operatives.

FBI officials are furious at Kelly over Monday’s raids because the NYPD seemed intent on scaring off the cell – which is believed to be plotting a New York attack.

The FBI hoped to wait and determine what the Colorado cell was planning.

Two other sources confirmed the FBI-NYPD rift. An investigator involved in the case said Kelly prefers to “act too soon rather than act too late.”

NYPD spokesman Paul Browne said it is “an utter fabrication that the FBI is furious with Kelly or that Kelly fought to shut down the action early.”

(Source: NY Daily News)