The Country Fire Authority (CFA) was called to the blaze just before 6:00am (AEDT).
The fire is burning in an inaccessible part of the mine, called ‘the knob’, but the operators are helping firefighters construct an access track.
Firefighters are going in on foot to battle the blaze which is about 20 square metres.
A helicopter was earlier called but has since been cancelled as the blaze is now under control.
In February, a fire broke out in the mine which burned for 45 days, covering Morwell with thick, acrid smoke.
In the first week of the fire about 20 firefighters were treated for carbon monoxide poisoning, while vulnerable residents were advised to leave the town weeks later.
Victoria Police are still investigating the cause of the February fires.