Det Supt Jason Murphy said: "Sadly we can confirm that three people have lost their lives in this fire."
He added the emergency services were "carrying out an extensive examination of the property to establish the cause of the blaze and determine if any other persons have been involved".
Firefighters said they were called to a "well-developed fire in a detached bungalow".
The blaze was reported to the Northern Ireland Fire and Rescue Service shortly before 07:15 GMT on Tuesday.
Two fire appliances from Lisnaskea and one from Enniskillen attended the incident the fire has now been extinguished.
The search is continuing.
