A firefighter needed surgery after a tiny finger cut became infected amid union concerns the water being used to fight a Victorian coal mine fire is toxic.

Fire Services Commissioner Craig Lapsley says authorities believe the water is OK for fighting the Hazelwood open-cut mine fire and that the testing regimen is correct but it will be re-examined.

The firefighter ended up with a serious injury requiring surgery after a very small finger cut became contaminated and his hand and arm swelled up.

Mr Lapsley said it was believed to be an isolated incident.

"I'm confident the test regimes are correct," he told reporters in Morwell on Friday.

"They are water sources that are not drinking water sources but are able to be used for firefighting.

"We'll take further advice today on whether any of the operation of the fire has deteriorated the water supply."

Melbourne firefighter and United Firefighters Union representative Mick Tisbury said the union paid $9000 to organise testing of water from a dam being used in the fire fight.

"Quite frankly these results are horrific," Mr Tisbury told ABC Radio.

An occupational hygienist detected extreme levels of bacteria and that could cause septicemia through cuts, Mr Tisbury said.

"The water they are using to attack the fire is toxic water," he said.

EPA Victoria CEO John Merritt said authorities have been sampling the water throughout the month-long fire fight in the coal mine.

"We are looking at this sampling in light of this incident to see what else needs to be assessed to make sure we're giving the best support we can to fire crews."

The fire has been sending thick smoke over the town of Morwell since February 9 when a deliberately-lit blaze spotted into a worked-out section of the Hazelwood open-cut coal mine.

Firefighters hope to have the blaze controlled by the end of the long weekend.

Victoria's Chief Health Officer Rosemary Lester said the temporary relocation advice for vulnerable people in Morwell South, the area closest to the mine, will then be reassessed.

"The improvement in the air quality is very encouraging, with continued progress on the fire," Dr Lester said.