FARMERS in northern Victoria and southern NSW remain under threat today as flooding caused by record rain worsens.

The return of clear skies over the weekend revealed record amounts of slow-moving brown water which have shocked authorities and communities battling to shore-up town levees and protect thousands of residents.

Northern Victorian towns of Nathalia, Walwa and Numurkah are encircled as the flood moves downstream towards Wangaratta and Shepparton.

The swollen Murrumbidgee River at Wagga Wagga has caused thousands of residents to be evacuated.

The National Farmers' Federation already estimates the damages bill from the flood could top $1 billion. It is the third major flood to hit Victoria and the Riverina in 18 months.

The Bureau of Meteorology is warning of the potential for more flooding in Gippsland.

The forecast is for fine weather in the North East but as much as 70mm over the next three days in areas of Gippsland which have already had 100mm or more of rain in the past week.

Agriculture Minister Peter Walsh said Department of Primary Industries staff were already on the ground assessing damage and helping with animal-welfare issues.

A DPI flood response management centre has been established at Tatura.

It is still too early to know exactly where to direct help, Victorian Farmers Federation president Andrew Broad said.

"This is not a flood event like last year which won't do anywhere near the damage but we have to wait and see," Mr Broad said.

He said a fodder drive would be launched to help struggling farmers similar to the response to last year's floods.

The Murray Dairy group and processors - Murray Goulburn, Fonterra, UDP and Tatura Milk - are helping co-ordinate the movement of cattle on to neighbours' farms and advising on stock management.

Cobram orchardist Noel Fisher said his 240mm was one of the biggest rain events he had seen since one episode of "eight inches in the mid-to-late '80s".

Australian Bulk Alliance general manager Simon McNair said the bulk handler's storages at Goolgowi and The Rock in NSW had some "water inundation" but it was too early to assess damage to grain quality.

Yarrawonga olive grower Franc Vodusek said it was the biggest rain in 50 years: "This is unbelievable."

Kutunga dairy farmer Daryl Hoey said the impacts of the flood could be greater than the devastating 1993 floods.

Rain records have taken a hammering with Rutherglen recording its highest eight-day total (261mm) since records began a century ago.

Yanco (259.6mm), Wilcannia (238.8mm), Albury (256.4mm) and Wagga Wagga (188.6mm) also broke eight-day records.