Frantic works have been done this week to build a levee around Echuca in Victoria's north-east to protect the town from flooding, but elsewhere existing levees have failed.

There are concerns levees downstream will suffer a similar fate with communities angry following years of lobbying to make sure their homes would be protected.

On Tuesday emergency permission was given to repair and fortify flood levee banks at Torrumbarry, north-west of Echuca, to prevent the Goulburn River from flooding the region.

Victorian leader of the Nationals and Murray Plains MP Peter Walsh said there were "some real challenges" in getting permission to fix the levee at Torrumbarry through relevant government departments.

"But that was granted [on Tuesday], and common sense has prevailed," he said.

Another emergency approval for works downstream of Koondrook, north-east of Kerang, was granted on Wednesday to raise the levee above 1975 flood levels.

"There's a similar issue to what would have been at Torrumbarry, where a levee has failed because the rivers eroded away," Mr Walsh said. 

Mr Walsh said communities were frustrated as they've tried for years to get these levees fixed, with claims that Parks Victoria and the Department of Environment Land Water and Planning (DELWP) had "been a blocker for years".

"But that's the only time you can elevate it to get decisions made.

"And I think that's just a tragedy for all the communities that are affected."

Policy to work 'with environment'

When contacted by the ABC, both Parks Victoria and DELWP said the responsibility of these two levees was with the Northern Central Catchment Management Authority (CMA).

The Northern Central CMA was contacted for comment but did not respond before publication.

The 2016 Victoria Floodplain Management Strategy developed by DELWP, appeared to move the focus of flood mitigation away from engineered structures, such as levees and culverts, to other options.

"There is a bigger role for non-structural measures such as land-use planning, flood insurance, flood warning systems, flood education and flood awareness," the strategy said.

It says there are high risks "with unmaintained, low-construction-standard levee systems" and "spending funds on levees … without understanding their full costs and benefits doesn't make sense".

"It is time to rethink and reset the approach, working more with the environment to allow wetlands to reduce the impacts of flooding by holding and slowing floodwater at appropriate times," the strategy said.

Other levees fail

Over the weekend, the Loch Garry levee also broke in several places amid criticism from locals that Goulburn Murray Water left it too late to open the gates.

Downstream of Loch Garry, north-west of Shepparton at Wyuna, dairy farmer Russel Pell said there had been significant levee breaching on the northern side of the Goulburn River.