Authority member Claire English said not only did it breach provisions of the Wages Protection Act, but it was also contrary to the terms of the contract the employer and employee had both signed.
"It is not open to Mr Donaldson to reduce Mr Babe's salary by deducting from it, or otherwise taking into account notional sums for items such as accommodation, power, annual leave and so on," she said.
Donaldson did not dispute the fact he owed Babe money but said the drop in salary was due to cashflow problems with the business and his own "deliberate and unilateral" decision to pay a salary significantly less.
The business had been in a poor financial position due to the impacts of Mycoplasma bovis which had recently been detected in New Zealand, he said.
Babe, who was on a two-year work visa, also claimed for compensation due to hurt and humiliation, and told the authority he had been forced to ask multiple times for his wages, which he found "embarrassing".
He had sent the money back to the Philippines to support his family.
Babe said the impact of being short paid was not just felt by him, but he also found it embarrassing trying to explain to his family why he could not support them.
His family in turn suffered hardship as a result.
English said Babe should have been able to rely on his employer to pay him as it had promised and in accordance with the law.
The authority ordered Donaldson to pay Babe $21,939.52 unpaid salary, $5000 holiday pay, $5000 for hurt and humiliation, $1380.60 gross in unpaid minimum wages and $7000 gross in costs.
The company's registered address is in Mosgiel, but the farm is in Mid-Canterbury.