Cracroft-Wilson was later handed a letter which called him to a meeting.
"We are writing to advise you of the seriousness of the situation which has been brought about through a "lack of management" and "good stockmanship"," the letter read.
"We view this as serious misconduct that MAY justify summary dismissal."
The meeting was held and Cracroft-Wilson was sacked a few days later.
The letter of dismissal stated Cracroft-Wilson should have been able to identify the declining health of the stock and taken action to address it.
"The opposite occurred. After some stock had died, you did not take any measures to prevent more deaths, understated the condition of the stock or seek assistance if the matter was out of your experience and knowledge.
"Therefore we have come to the conclusion that the lack of judgement shown by you amounts to serious misconduct, justifying summary dismissal."
Cracroft-Wilson approached the Employment Relations Authority (ERA) in Christchurch claiming he had been unjustifiably dismissed.
He said he had limited knowledge of Yersinia before the outbreak and claimed that stress created by drenching in inappropriate weather may have caused the deaths.
His decision not to feed stock on certain days after the first deer were found dead was because he knew stress could increase the animals' susceptibility to Yersinia.
After a tribunal hearing in December, ERA member M B Loftus has now ruled in the worker's favour.
"A failure to practice processes or to apply limited or lacking knowledge is not serious misconduct," said the ERA in its determination.
It was unacceptable for Hood to have assumed that Cracroft-Wilson should have known about Yersinia simply because he had spent a lot of time in the industry, it said.
Hood acted too hastily in its dismissal of Cracroft-Wilson and Hood should have taken other steps if he thought his worker's actions were not up to standard.
Mt Hutt Station was ordered to pay Cracroft-Wilson $7307 as recompense for wages and $5000 as compensation for humiliation, loss of dignity and injury to feelings.