Another witness said he heard Mr Clarke say: "I'm going to come back with a gun and shoot you all."
Mr Clarke was suspended on pay from June until September while an investigation was carried out.
Police were also notified and issued Mr Clarke with a warning.
At a disciplinary meeting in July, Mr Clarke said he had made the comments out of frustration and to lighten the mood, saying: "Maybe a shooting spree would sort it all out."
He said that was met with a round of laughter and a colleague had jokingly replied: "I'll make sure I'm far away when you do."
At the second incident, Mr Clarke accepted he had been frustrated and had raised his voice.
But he said he had not directed his comments at anyone, saying: "This is bullshit, I may as well just go get a gun and blow my head off."
Mr Clarke accepted he had not chosen the right words and apologised for what he had done.
Air New Zealand's investigation concluded Mr Clarke's comments were made in the form of a threat and amounted to serious misconduct.
The comments were highly inappropriate and Mr Clarke would have been aware of the high sensitivity around safety and security matters in the airline industry.
Mr Clarke took his case to the Employment Relations Authority, arguing the investigation into the incidents took too long and had not taken into account the culture of jokes in the workplace.
Authority member Greg Wood found while Mr Clarke's length of suspension was not ideal, the investigation was not unduly long as there were issues contacting a number of witnesses.
He accepted there was a culture of jokes in the workplace and Mr Clarke had no intention of carrying out his threats, but said his comments were made in a serious manner.
Mr Wood found Mr Clarke's misconduct was particularly serious in the security conscious environment of the aviation industry and his dismissal was justified.
Costs were reserved.