The climate change sceptic scientist Peter Ridd has been awarded $1.2m in compensation after winning an unfair dismissal case against his former employer, James Cook University.

In April federal circuit court judge Salvatore Vasta found the actions of the university, including Ridd’s repeated censure and ultimate dismissal, were unlawful.

Vasta handed down a penalty on Friday and ordered the university to pay Ridd more than $1.2m for lost income, lost future income and pecuniary penalties.

Guardian Australia understands the university intends to appeal the judgment. It has three weeks to lodge any appeal.

The case has been repeatedly framed in media reports as one about academic freedom, or about the validity of the minority and controversial views held by Ridd about climate change and the health of the Great Barrier Reef.

Vasta made clear in his judgment in April those matters were not on trial.

“Some have thought that this trial was about freedom of speech and intellectual freedom,” he said. “Media reports have considered that this trial was about silencing persons with controversial or unpopular views.

“Rather, this trial was purely and simply about the proper construction of a clause in an enterprise agreement.”

Vasta’s ruling on Friday determined the extent of the economic loss suffered by Ridd as a result of his censure and dismissal. The scientist, who has endeared himself to some in the Queensland agricultural sector for arguing against the consensus view that farm pollution is damaging the reef, argued in court that academic institutions would not hire him.

During the hearing, it was put to Ridd that he had received widespread promotion as a result of the case, and that this had in effect helped to maintain his reputation.

“No, quite the opposite,” he said. “In terms of the companies that want to hire scientists, all the fame and being on the Australian [newspaper] or on the IPA doesn’t help one iota. I think it’s bad. I mean, maybe that will produce a different career outcome but in terms of these sort of things most big institutions don’t want a bar of somebody who has been through my sort of controversy.”

Vasta agreed that Ridd was “damaged goods” and had poisoned the well for Ridd’s future employment prospects.

“The fact that JCU has not removed either of their press statements (despite my judgment) is almost tantamount to an attempt to ensure that Professor Ridd does not obtain employment in this field,” he said.

Despite the judge’s earlier comments that it was not, Ridd said in a statement that the case “was always about academic freedom”.

“If JCU appeals it casts doubt that academic freedom is part of their DNA as they often insist,” Ridd said.

“An appeal will continue the huge and pointless legal costs.”

Ridd has recently held a series of lectures in regional Queensland, promoted by cane growers’ groups and the climate-sceptic Australian Environment Foundation.