During Crowley's allegedly inebriated testimony, he revealed to authorities that the 5-month old baby may be buried.
As deputies were headed to the scene, additional calls came in saying the man was threatening people and saying he had a gun, the release said, and was reaching in his pockets.
When deputies found the man, he said a baby who was in his care hadn't been seen for several hours.
While attempting to locate Crowley, a 911 caller said the suspect had returned to the hot springs. During questioning, he appeared to be under the influence of drugs and indicated the baby was buried somewhere in the mountains.
A collaborative effort including officials from the United States Forest Service, Missoula County Search and Rescue, the Bureau of Land Management, the Montana Highway Patrol, and Missoula County deputies then set off in search of the missing 5-month-old who was finally found at about 2:30 a.m. Sunday morning.
The five-month-old baby who was abandoned Saturday in a remote area near Lolo Hot Springs is said to be in good condition at a Missoula hospital.
Police have charged 32-year-old Francis Crowley with criminal endangerment, and more charges are expected, reports the Missoulian.
"Sheriff (T.J.) McDermott would like to thank those who assisted in the search and those who called 911, helping first responders bring this baby to safety", the statement said.
Searchers followed the sound and found the infant alive, buried facedown beneath a pile of sticks and debris. The infant was only wearing a "wet and solid" onesie as he endured 46-degree temperatures for at least nine hours, according to police.
"He suffered some minor scrapes and bruising but overall is in good health", sheriff's spokeswoman Brenda Bassett said in a statement.
'For the officers who were present for this event, its especially hard knowing what this small baby endured in the last 24 hours'.
The child had been in the care of Francis Carlton Crowley, 32, on Saturday, according to the release.
Authorities have not yet released information about the relationship between Crowley and the baby, nor released any information about the mother of the baby.
Crowley has now been charged with criminal endangerment. When they arrived they learned the baby had been missing for several hours and Crowley had vanished.