Black Hawk County sheriff, Capt. Rick Abben, did not divulge details as to exactly where the bodies were found, the Associated Press reported.
Reports indicate that 9-year-old Elizabeth Collins and 11-year-old Lyric Cook were last seen alive on July 13 near a recreational lake in Evansdale, a city about 110 miles northeast of Des Moines. Investigators found their bikes and a pink purse near the lake hours later, but no sign of the girls.
"It's definitely not the outcome that we wanted, obviously," Abben said during a news conference in Evansdale. "This is a difficult thing for us to go through. It's a difficult thing for the community."
An emotional Abben added that the bodies were being sent to the state medical examiner’s office to confirm their identities.
The families of the two girls have been notified of the discovery and are asking for privacy, according to police.
In the days after the two Iowa cousins went missing, hundreds of volunteers helped investigators in a search that spanned cornfields and wooded areas in and around Evansdale, a city of 8,000 residents.
The FBI also aided in the search by bringing n specialized equipment to search the bottom of the lake for the girls but found nothing. Police later said they believed the girls had been abducted.
While authorities have remained tight-lipped in the months since the search, an FBI spokeswoman did tell reporters it had reason to believe the girls were alive.
According to the AP, authorities had asked hunters to keep a lookout for the girls in the region during this fall's popular deer hunting season.
Abben said the bodies were discovered around 12:45 p.m. Wednesday, but refused to say where, saying the area was still being processed as a crime scene and could not be compromised.
"Preservation of that scene is paramount," he said.
Abben said he hoped to release additional details on Thursday.