Morenci Chief Larry Weeks is now asking people in the area, along the Michigan-Ohio border, to be on the lookout for bodies. He said investigators have followed up on 900 tips but they have not been fruitful.
"We've seen false hope continue to grow," he told reporters.
Weeks said the boys' father, John Skelton, is the primary focus of the investigation, although no new charges have been filed. Skelton already has been charged with parental kidnapping and is being held on a $30 million bond.
Lawyer John Glaser, who is defending Skelton in the kidnapping case, did not immediately respond to a message seeking comment.
Nine-year-old Andrew, 7-year-old Alexander and 5-year-old Tanner were last seen playing on Thanksgiving in their father's backyard in Morenci, about 70 miles southwest of Detroit.
Skelton's estranged wife, Tanya Skelton, reported her sons missing the next day after they weren't returned to her. John Skelton said during a custody hearing in December that he gave them to someone from an "organization" that he wouldn't identify. Investigators have said he earlier made false claims about turning his sons over to another woman.
At a court hearing last week, John Skelton said, "I can't," when a judge asked if he was prepared to give the boys to their mother. He didn't explain why not.
Weeks has said for months that he didn't expect a positive outcome. The reason to no longer call this a missing persons case, he said, was based on what Skelton has said in past interviews with investigators.
That includes telling police that he gave the boys to a group called United Foster Outreach and Underground Sanctuaries, Weeks said.
"No such organization can be located," the chief said. "That's just one example of misinformation that we received from him."
Tanya Skelton had continued to hold out hope that the boys were alive until investigators said that they were changing their focus.
"It's like somebody cut your chest open and yanked your heart out," said Kathye Herrera, a family friend.
The fate of the boys has consumed not only this small town where faded yellow ribbons are tied to trees, but also communities nearby in Ohio and Michigan.
Busloads of volunteers searched fields and vacant homes for the boys for a week after they disappeared. Dive teams checked ponds, lakes and rivers in both states.