The body was found at about 10:00 p.m., on Monday.
Police have not given the exact location of the recycling container, but indicate it was not far from the Clayton girl's home.
The Medical Examiner will conduct an autopsy on Tuesday to confirm the body's identity.PHOTOS: WEBSITE and iPAD | WIRELESS
"This is a very sad day for the Pasquale family," Gloucester County Prosecutor Sean Dalton said. His office led the search with assistance from 20 municipal, state and federal agencies.
"Our hearts go out to the family and to all the residents of Clayton who stood together in support of this young girl."
Autumn's family reported her missing on Saturday night at around 9:30.
Two hundred law enforcement personnel had been working on the case, along with dozens of volunteers who helped in the search.
Police say they are now conducting a criminal investigation, but so far, have not indicated if they have any suspects in mind.
Among other things, they are reviewing information on every sex offender in the South Jersey area.
The Child Abduction Response Team (CART) has been activated. They have pulled records of every registered sex offender in the area and they are looking at surveillance video from around town.
Autumn went for a bike ride around 12:30 p.m. on Saturday, and had not been seen since.
The FBI, NJ State Police and the Gloucester County Prosecutor's office are among the agencies involved.