Heavy rainfall has prompted widespread flooding across the Gippsland region.

The Latrobe River to the north of the mine has reached moderate flood levels, and minor flooding is occurring in the Morwell River to its east.

Operators EnergyAustralia on Friday afternoon ordered all people to leave the mine and removed equipment as a precaution.

The power station continues to run, but output has been cut to conserve coal while the flood situation is monitored.

In 2012 the Latrobe River broke its banks and entered the mine forcing it to close for weeks.

Head of Yallourn Julian Turecek said coal production at the site would recommence as soon as it is safe to do so.

"Yallourn's generation output is being maintained at an appropriate level... safety is our highest priority," he said in a statement.

Gippsland Trades and Labour Council secretary Steve Dodd told the ABC the coal cache could run out in three days.

He is also concerned the rivers could break their banks again, prompting electricity supply fears.

But the Australian Energy Market Operator has moved to quell those concerns.

Power supply is sufficient to meet demand nationwide and the system is currently not at risk, a spokesperson said in a statement.

"Victoria currently has a strong reserves position, and AEMO forecasts show no foreseeable reserves issues in coming days," they said.

Australian Associated Press