Parts of east Gippsland recorded nearly 300 millimetres of rain, over the weekend, according to the Bureau of Meteorology.
Major flood warnings were issued for the Cann and Genoa Rivers, after above average rain in the area in recent months, says Bureau of Meteorology duty forecaster Miriam Bradbury.
"The focal point of rainfall was central and east Gippsland, pretty much from the Gippsland Lakes eastwards, but the highest rainfall were seen in the easternmost parts of east Gippsland," Ms Bradbury said.
In the 48 hours until 9am, today, Mount Cann fire tower recorded 287mm, Mt Waldron fire tower, 278mm and Club Terrace had 204mm.
"Across that 48 hours, Malacoota saw 184mm and Orbost 171mm."
"It was a really deep low pressure system, which moved from the south-east NSW coast, down across Bass Strait."
As it came nearer the Gippsland coast, it pushed fresh to strong south-west across the region and also brought "very significant rain systems."
The low pressure system was now moving across the Tasman Sea.
"We only have two moderate flood warnings, the Snowy and Mitchell Rivers, and a number of minor flood warnings.
"We did see a number of flood gauges, spiking in that area overnight and early this morning, getting close to the major flood level," she said.
The Cann River experienced moderate flooding, peaking at 3.89 metres at Weeragua on Sunday night.
"Even though the warnings have been downgraded to moderate, the flooding impacts are still continuing across that area.
"A lot of that water is moving downstream, so we may see further changes to those warnings."
But Ms Bradbury said there would be a few days of respite, with only light showers, before another trough crossed the state on Wednesday.
"The showers on Wednesday are not expected to bring massive rainfall totals - currently we are looking at only 5-10mm across west Gippsland, possibly reaching 20-30mm in those very far parts of east Gippsland.
"It is obviously still highly sensitive and one we will be monitoring closely, not just the rainfall but the flood situation as well."
Watch and act warnings have been issued for communities near Cann River, Buchan River, Bemm River, Genoa River and the Snowy River downstream of McKillops Bridge.
The same alerts have also been issued for the Mitchell River to Glenaladale and the Tambo River.
Meanwhile, the Princes Highway between Orbost and Cann River is now open in both directions following a closure due to severe weather overnight.
The Princes Highway between Cann River and Genoa remains closed however with crews still working to clear the road.
The Monaro Highway is now open between the NSW border and Cann River.
The township of Bemm River remains isolated with crews still working to reopen access.
Marlo Road is closed to traffic however local traffic may use Cabbage Tree-Conran Road to get access in and out of Marlo.
More than 20 other roads managed by the Department of Transport are also closed including Bengworden Road at Chinns Bridge and Tom's Creek.
Emergency services continue to assess damage to roads.
More roads may need to close roads at short notice.
Detour routes may not be available or suitable for all vehicles.