Tragowel dairy farmer Catherine Shepard likened the process to a rabbit with a carrot dangled in front of its face.
“Farmers are the rabbits and this particular rabbit feels like the carrot just keeps getting dangled in front of us in hard times,” Ms Shepard said.
“I am sick to death of having hope ripped out from under me and then in the next sentence told if I need help call a counsellor.”
The program is being implemented in two parcels, 40 Gl now and 60 Gl in the new year.
Ms Shepard said she was happy for those that were successful, but in a tough year it had left those that missed out feeling "terribly dejected".
“Things are really bad and unfortunately some people may not be able to wait until next year to apply for the ballot again.
“Many people are facing huge business decisions in the coming months.”
She also questioned why the world’s best quality food, Australian produce, was not valued by the country’s leaders.
“I think every farmer in this country of ours is worth a lot more than some form of ballot to keep our home-grown produce growing and our Aussie family business running.”
Katunga dairy farmer Emily Brown said while the program was easy enough to apply for, it was a bit like throwing out scraps.
“I don’t think they should have done the program at all if they couldn’t give water to everyone,” Ms Brown said.
“The people that missed out feel bad and I am sure the people that got it probably feel bad as well.
“We applied because we would have been silly not too, but it never sat right with me.
“I am sure the government are feeling really good about being seen to be doing something, but the reality is there are more people feeling bad than good.”
She also hoped the missed opportunity did not affect the mental health of the region's already struggling farmers.
Beck Wolfe from Peacocks Transport & Hay Contracting at Rochester was one of the successful applicants.
She said the 50 Ml ensured the family business would be able to water up at least one hay crop this year.
“At least we know we will get something — we have been one of the lucky ones.”
Of the 2554 Victorian applicants 504 were successful, while NSW had 1574 applicants and 283 were successful.
South Australia, whose irrigators are on 100 per cent allocation, had 57 applicants and 13 were successful — the highest rate of 23 per cent.
Federal Water Resources and Drought Minister David Littleproud said the response showed just how keen farmers were to participate.
“Farm businesses are looking for ways to earn a quid during the drought and we’re providing that with Water for Fodder,” Mr Littleproud said.
“This water is only for growing fodder, silage and pasture. Fodder cannot be a by-product,” he said.
“Farmers who have missed out will have another chance with 60 gigalitres available in the new year.”
First round assessment will guide how the remaining water is allocated.
