The hotspots were detected by thermal imaging — incident controller Mark Mawhinney said ground crews with hand tools worked to extinguish seven, while helicopters were "waterbombing" the other six, which could not be accessed on the ground.
Helicopters were stood down as strong winds hit the area at about 4pm and ground crews had withdrawn at 5pm.
No new fire activity was detected today and steady rain has been falling on the site since late afternoon.
Fenz would be monitoring the site tomorrow but did not plan to have crews on the ground.
After the rain, conditions would be too slippery for firefighters to work safely on the steep slopes, Mr Mawhinney said.
Emergency services were first called to the fire about 4.35pm on Friday.
By Saturday night, it had grown to about 200ha, in the Twenty Five Mile Creek area, and was initially fought by eight helicopters and four ground crews.
On Sunday, seven ground crews and six helicopters continued to battle the blaze, which had grown to about 230ha, destroyed the land on Mt Crichton Station and reached an area managed by Department of Conservation.
A further update is expected this evening, meanwhile, Mr Mawhinney said the "mopping up" would continue tomorrow.
