The Primary Industry Training Organisation says it believes most farmers taking on workers who have gained qualifications through the organisation are satisfied with the standard of training.
Some farmers have expressed concern that workers were not able to perform basic skills that their qualification said they could do and there was inconsistency in training.
Primary ITO chief executive Mark Jeffries said the feedback from employers was fairly positive.
"Pretty much everyone is supportive of the programmes we have to offer, and in saying that, we are not dodging the conversation we are having now with Federated Farmers - clearly some farmers are not happy with the results they are seeing from the trainees with their pieces of paper.
"Most farmers are prepared to recommend us services and our certification to neighbours, to other farmers and trainees. So I don't think there is a big issue that's undermining the system. What is important here is that there is an expectation that's not being fulfilled by some farmers," he said.
"Part of the problem is the training system in where we can promote and clarify what expectations the employers can expect. Promote the pathways that the trainees can fulfil with the variety of certification products that are available, but also the farmers themselves.
"We know that there are many farmers that can provide a better environment to their trainees conducive to life-long learning opportunities. We need to see farmers promoting confidence in their trainees. This conversation is around matching farmers who are prepared to give trainees those sort of environments with trainees who are prepared to respect their employers."
Federated Farmers said it was not losing faith in the Primary Training Organisation. However, the chair of its meat and fibre section, Rick Powdrell, believed some refining of training was necessary.
"You have to remember that there are a number of providers and so it's getting consistency across the providers and it applies to not only training the prospective employee but it's consistency of assessing and also training trainers, and assessing trainers, It's the whole gambit really."