Abben wouldn't say where the bodies were found, and said they were being sent to the state medical examiner's office for identification. He said he hoped to release more information Thursday.
"It's definitely not the outcome that we wanted, obviously," said Abben, appearing to fight back tears. He spoke at a news conference in Evansdale, where the girls had been staying with their grandmother when they disappeared.
"This is a difficult thing for us to go through. It's a difficult thing for the community," he said.
The cousins disappeared July 13 near a popular recreational lake in Evansdale, about 110 miles northeast of Des Moines. Investigators found their bicycles and a pink purse near the lake hours later, but no sign of the girls.
On Wednesday night, about 70 people attended a prayer vigil at the lake, some cradling plastic cups with candles to protect the flames from the cold wind. Some were holding out hope that the bodies weren't those of the missing cousins, though others seemed resigned to accept tragic news.
"I don't want to think the worst, but two bodies. It's just really heartbreaking," said Amanda Mulzac, who lives in nearby Waterloo and was among hundreds of volunteers who helped in the initial search. "At their age I was out by myself, but now it's different. Hold your babies close."
Barb Collins, a machinist who grew up in Evansdale and helped lead the group in prayer, said the community was grieving.
"These were just innocent children. These girls should have been left alone. They should be home safe in their beds, and it's only a coward who would have done something like this," she said after the vigil.
Abben declined to say Wednesday if there were any suspects in the cousins' disappearance.
Hundreds of volunteers helped investigators to search for girls, traipsing through cornfields and wooded areas in and around Evansdale, a city of 8,000 residents. The mayor even joined the search in his private plane.
Days later, an FBI dive team brought in specialized equipment to search the bottom of the lake for the girls but found nothing. Police then classified the case as an abduction.
Investigators had largely been tight-lipped in the months since. An FBI spokeswoman initially said investigators had reason to believe the girls were alive, but other investigators backtracked, saying only that there was no reason to believe the girls were dead.
Authorities had asked hunters to look out for the girls 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. He said 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 the girls' families wanted to express gratitude to the community for their support but have asked the media to respect their privacy at this time.
Investigators have poured through thousands of tips and chased multiple theories in the case.
They looked into Cook's parents, who had criminal records for prior involvement in making methamphetamine. Cook's father, Daniel Morrissey, is being prosecuted for domestic assault and a series of meth and other drug charges, and he backed out of a plea agreement with prosecutors the day before the disappearance. They have denied any involvement.
The region had rallied in support of the girls. Photographs of the cousins seemed to be everywhere in northeastern Iowa: on T-shirts and buttons worn by locals, and on fliers hung on gas station walls and in business windows.
Residents held prayer vigils, even as the months passed. Last week an anonymous donor pledged $100,000 for information about the girls' whereabouts, on top of the $50,000 that police had offered.
After Wednesday night's vigil, family friend Sarah Curl said it was a tight-knit, caring community.
"When something happens to one family it happens to all of our families," Curl said. "This could have happened to anyone."