Farmers in the Rochester and Loddon Valley irrigation districts claim the failure of automated watering equipment is playing havoc with their winter planting plans.
Mixed and dairyfarmers say they are increasingly frustrated with fluctuating supply levels.
They said expensive equipment - Magflow meters supplied by Rubicon Water at a cost between $30,000 and $50,000 - was constantly breaking down.
Fernihurst farmer Laurie Maxted said because the Loddon Valley was flat, irrigation channels were widely spaced apart.
"The Rubicon system starts at the bottom and works back, it 'talks' to the pool upstream from it, it has to open up and fill up that pool, then goes back to the next one," Mr Maxted said.
"It's taking all the water to the bottom, and slowly and surely filling it up.
"We begged and begged for years for them to leave the Dethridge wheels there - for two or three hundred dollars, they could have changed the calibration on the tumbler."
Fernihurst's Ken Pattison said irrigators felt they were "over a cliff - we are in freefall".
"We have been given no figures as to what the contract details are, we have no idea what is being paid to Rubicon. There is no line item as to what they are paying them to maintain the system."
He said Goulburn Murray Water had been forced to take some channels out of automatic mode and operate them manually.
"We have a modernised system, plagued with costly breakdowns and repairs and the ongoing maintenance of system is of great concern to remaining GMW customers," Mr Pattison said.
Durham Ox mixed farmer Murray Haw said it appeared there were problems with what was known as the total channel control (TCC) system.
He said he was watering lucerne crops from a backbone, off the main channel.
"You get these wild fluctuations, from 10 megalitres (ML) to to zero in a four-day period," Mr Haw said.
"The doors will open up and drop the whole pool, and we will have nothing. It could take half a day to fill the pool up again."
At Echuca West, cropper Glenn Murrells said he was getting "an extremely variable" supply, out of what was supposed to be an upgraded, auto-flow backbone channel.
"There is a 40 per cent change in the flow rate, over a 20-hour period," Mr Murrells said.
"The problem has to be with the auto regulators on the channel, which are letting the pools run too low."
Mr Murrells said he had one meter, on his property, which was rated to flow at nine to 10 megalitres a day.
"It's only achieved seven, at best - this is on a lucerne paddock and it's very detrimental when you get slow flow rates; you want it as fast as possible."
Farmers also said there were issues with vermin, including rats, and ants getting into the automated control boxes and destroying wiring.
"I had two blokes come out, for a whole day, to repair one," he sid.
"I asked why they didn't do them all - they replied they had enough work for 25 years, so why would they?"
In 2010, dairyfarmer Mark Bryant spent $350,000 on upgrading and modernising his 280-hectare farm, at Waaia.
"I think, reading between the lines, those that got done early, are happy enough, but for those being done, between the change of government, twice, it's been a disaster," Mr Bryant said.
He said he was on a backbone along the Nathalia-Katamatite road.
"Ours is still the original channel, we get a seven megalitres flow, but the channel leaks like a sieve, because it's clay, so it cracks and seeps."
Mr Bryant said, for preference, he would dry the channel off, because the Broken Creek ran 200 metres from it.
"You could put pumps on the creek - it would be very simple and save millions of dollars," he said.
"They were going to modernise it, then they were going to decommission it, and pump off the creek, then they were going to divide it into lots, and now they are going to put a new $50,00 magflow in there, which will give me seven ML a day, when a wheel can give me 10ML."
Rubicon referred questions to GMW, with managing director Pat Lennon saying routine maintenance would pick up instances where channel levels "were not maintained within our service standards".
He said work was being done on computer hardware and software programs.
"It's not unusual to intervene manually, while we follow through and change some settings on channels, that's all it is," Mr Lennon said.
"It's not something that is irregular - it's not uncommon to see a manual intervention, while we tune the software, and the management of the channels."
Mr Lennon said the systems were "very complex in nature" and getting the hydraulics right, took time.
"Sometimes there is an empirical side to it, you observe the channel behaviours, under certain off-take conditions, and then you look at what the meter was saying, and then you make some changes, having acquired that knowledge."
He said rodent and insect control was part of the usual maintenance program.
"We have applied a different seal method in one of the places, it's not a major issue and we don't see that in every location," he said.
"There is a slight modification to one of the covers, as part of the system."