Hamilton police say an autopsy is set to be conducted today on a boy who was found dead after going missing over the weekend.

Police and neighbourhood volunteers spent much of the weekend searching for Finnigan Danne, who was last seen on Saturday morning at his home.

The 12-year-old boy suffered from a neuromuscular disorder, walked with a significant limp and had limited mobility without a wheelchair.

Police issued an Amber Alert for Danne -- typically used in cases of suspected child abduction -- on Sunday afternoon, but cancelled it less than an hour later.

They said Danne had been found dead, though they would not confirm reports from neighbours that the boy was located in or around a culvert not far from his home.

Police said officers, a mounted unit, ATVS and dogs were used in their search for the boy.

A police spokesman said no further details would be released about the case until the results of Danne's autopsy are analysed.

Residents in the Hamilton community of Dundas, where Danne lived, said they were shocked upon learning the boy was found dead.

"I'm stunned, because it was a really extensive search. The police were here on horseback yesterday, they went down there, I saw them do it," Moira Leggate told reporters after Danne's body was found.

"The police were here with the dogs from yesterday from about two o'clock. I was with them. We didn't leave anything unturned."