While lifting a cow's tail did not cause any distress the risk arose if excessive force was used, causing it to break.
The maximum penalty for the charges are 12 months' prison or a $50,000 fine.
The Ohaupo farm has a total of 516 cows in its herd.
In his earlier reserved decision convicting the company and McDonald, Judge Simon Menzies could not quantify the exact number of animals injured, rather confirming it was a "significant number".
In the Hamilton District Court yesterday, defence counsel Philip Cornege said given that finding, he urged him to sentence on the basis of one cow being injured for each charge.
He submitted that by suggesting that any more than one animal was injured would be nothing more than "speculation".
"Because your honour has made a finding that it's impossible to quantify it's then not possible to proceed on the basis of anything other than one in either category because anything else would be, in my submission, speculation.
"In relation to the categories there must be at least one that was caused by poor stock handling ... it can't be some imprecise number of the 119 animals."
More animals having their tails damaged was more serious than fewer for the purposes of sentencing, he said.
He asked the judge to issue fines of between $500 and $1000 for each charge.
Cornege suggested the breaks came about in a form of conduct he suspected that was being used "on almost every dairy farm in New Zealand which resulted in one or more tail breaks".
He described McDonald, 42, as an "exemplary farmer" and he, along with the company, deserved credit for their previous clean record.
The company had made multiple changes after charges were laid and more since being found guilty, he said.
MPI prosecutor Kevin Herlihy disagreed and noted in the judge's finding that with 36 per cent of the total herd suffering injuries "the only logical inference that can be drawn from this assessment is that a significant portion of the 36 per cent of tail breaks were caused by stock handling."
He said that was different to an inference of just one animal per charge being injured.
Judge Menzies disagreed with Cornege's submission and said he would sentence on the behaviour which caused the injuries rather than the number of cattle involved.
"I have an issue that I would approach it on the basis of saying that it's one animal in each category.
"What we've got is a situation where the findings establish that there has been a form of behaviour in, what your term was, the improper stock handling technique which led to the problem.
"It's more the pattern that's of concern and the behaviour generally ... it is not 10 times worse if you've got another set of circumstances where 10 animals are being mistreated. It's still the behaviour that has to be looked at and a common sense approach adopted as to how that is viewed."
In setting his fines, Judge Menzies said he consider it more appropriate that it was focused on a pattern of conduct that itself has involved improper stock handling.
The injuries occurred while McDonald had both physical and supervisory contact, he said.
"It has happened on his watch both in his capacity as a person in charge of the herd and a director of the company."
The prospect of further offending was remote, he added.
