Dr Ridd had disparaged colleagues'work as untrustworthy and"misleading"in correspondence with a journalist and in television interviews.
Dr Ridd's subsequent legal action against JCU's treatment of him has received significant attention in the media. Because of his outspoken scepticism of climate change science,the example has been at the centre of debate about the state of free speech in academia.
Judge Salvatore Vasta found the university's actions against Dr Ridd,including his dismissal,were all unlawful.
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Noting some coverage had painted the matter as an example of controversial views being silenced,Judge Vasta said the trial was"purely and simply about the proper construction of a clause in an enterprise agreement".
The judgement also said the university had failed to fully understand the importance of intellectual freedom.
In a statement,JCU provost Chris Cocklin questioned the judgement and said the university was"considering its options".