Officers used a pulley system to raise the jagged, 255-pound metal piece on Wednesday. Onlookers took pictures as it was loaded onto a truck headed to a Brooklyn police facility.
The part was discovered a week ago, wedged in a narrow space between an apartment building and a mosque.
Authorities believe the part is from one of the two hijacked planes that brought down the trade center on Sept. 11, 2001. Of the nearly 3,000 victims, remains of about 1,000 were never recovered.
Retired fire department Deputy Chief Jim Riches, who lost his son in the terrorist attacks, visited the site on Saturday. He said the latest news left him feeling "upset."
"The finding of this," he said, "just goes to show that we need federal people in here to do a comprehensive, full search of lower Manhattan to make sure that we don't get any more surprises," as happened in 2007 when body parts were discovered in nearby sewers and manhole covers.
The piece of wreckage was discovered by surveyors inspecting the planned Islamic community center on behalf of the building's owner, police said.
The twisted metal part - jammed in an 18-inch-wide, trash-laden passageway between the buildings - has cables and levers on it and is about 5 feet high, 17 inches wide and 4 feet long, police Commissioner Raymond Kelly said Friday.
"It's a manifestation of a horrific terrorist act a block and a half away from where we stand," he said after visiting the alley.
When plans for the center became public in 2010, opponents said they didn't want a mosque so close to where Islamic extremists attacked, but supporters said the center would promote harmony between Muslims and followers of other faiths.
The building includes a Muslim prayer space that has been open for three years. After protests died down, the center hosted its first exhibit last year. The space remains under renovation.
Detectives also solved a mystery about a piece of rope intertwined with the part. A responding officer on Wednesday used rope that he found on the ground nearby to wrap around the aircraft part in order to move it in such a way as to look for its serial number or other identifiers.
Police said the part will be moved to a more secure location, where a determination will be made about where it will go permanently.
CLICK HERE TO SEE PHOTOS OF THE PLANE DEBRIS (The Associated Press contributed to this report.)