"Our thoughts are very much with Matthew's devastated family who received this tragic news today”
It was found in the Fintona area shortly before 12pm on Monday.
The 15-year-old was from the Dungannon area.
PSNI Detective Inspector Michael Winters said: "Our thoughts are very much with Matthew's devastated family who received this tragic news today.
"A number of specially trained officers are providing support to them at this time.
"Detectives will continue to investigate the circumstances surrounding the death, which is currently being treated as unexplained.”
PSNI vehicles were stationed on the Tattyreagh Road outside Fintona where searches took place earlier on Monday.
The boy was last seen in the village at around 1.30am on Sunday after leaving a festive event.
A local GAA club that had been helping with the search effort took to social media to confirm it has been suspended and to thank everyone who offered assistance.
"Public volunteer search operations are suspended for the time being,” the post on Fintona Pearses GAA’s Facebook page stated.
"Thank you for you assistance so far.”
It was previously reported Matthew was last seen on CCTV outside a takeaway in the Fintona area getting into a grey car with a man wearing a black body warmer jacket.
He also was allegedly seen speaking to a taxi driver in a red car, whom his family are appealing to come forward should he have information about where Matthew was possibly headed.
"We are praying he is found safely,” they said. “Thank you for all your help and support so far, please continue to share. We are not stopping until he is found.”
A police spokesperson said on Sunday: “Police in Omagh and Dungannon are becoming increasingly concerned for the welfare of missing 15 year old Matthew McCallan.
“Matthew was last seen at around 1.30am this morning in the Fintona area.”
Anyone with information should contact detectives on 101 quoting reference number 319 4/12/22.