A Manhattan grand jury is investigating the Mafia’s theft of scrap metal from the World Trade Center rubble, law-enforcement sources told The Post.

More than 250 tons of crime scene material mysteriously found its way into three scrap yards this week, and investigators blame organized crime, a source says.

Material taken from ground zero at the WTC site is supposed to be held at the Fresh Kills landfill on Staten Island, where authorities are sifting through debris and conducting the largest crime-scene investigation in U.S. history.

But, law-enforcement sources said, some of the scrap metal was stolen and held at three scrap yards.

NYPD organized crime investigators are probing the case, along with the state Trade Waste Commission.

Investigators found 75 tons on Monday after searching Mid-Island Scrap Metal in Deer Park, L.I.

No one has been charged in the case, and sources said the yard’s operators allowed cops to search it.

An office worker at Mid-Island Scrap said the yard’s manager, whom she declined to identify, was “out,” and he didn’t return a call for comment.

Investigators later found a total of 180 tons at two yards in New Jersey, which they declined to identify.

A law-enforcement source said it’s believed that associates from some of the city’s five crime families – long linked to corruption in the waste business – are involved.

At least 10 suspects are involved in the thefts, the source said.

While the diverted evidence was a staggering amount of metal, it was also easy to miss – over 128,000 tons of debris has been hauled away from lower Manhattan since two hijacked planes brought down the gleaming towers.

Police sources said they believe the metal was taken directly to the yards by garbage trucks in the days immediately after the awful terror attack.

That was before the trucks were escorted to the dump or to floating garbage barges, and drivers were free to go wherever they wanted, one source said.

All of the scrap – with some single pieces weighing as much as 800 pounds – has since been returned to Fresh Kills, one source said.

Sources said the heartless and unpatriotic thieves who pulled off the massive theft wouldn’t have made a lot of money – they’d get $1.60 per 100 pounds of scrap, or just over $15,000 for all 255 tons.

The grand jury could charge the suspects with such crimes as tampering with evidence, obstruction of justice, theft and conspiracy, the source said. The Manhattan DA’s office refused comment.

The incident isn’t the first involving theft from the ground zero area. Looters have ripped off some of the vacated stores in the area, and some passers-by have taken pieces of debris off garbage and flatbed trucks as they go by.

Meanwhile, police and federal officials denied a published report that there was a nationwide search underway for a missing rented U-Haul truck.

“There’s no A.P.B. out and we don’t believe the truck has any bearing on the case at all,” the fed said. “People don’t return rental vehicles every day.”

They also denied a report that city officials have specific intelligence information about a tractor-trailer full of explosives headed for New York.

“That’s bull,” a top police official said.

The federal official also didn’t know about any such threat, and that the feds were “surprised” by the stop-and-searches being done on trucks in the city.

The police official said they’re simply “being cautious.”