In 2014 I purchased an off the plan apartment ion the Gold Coast in a company name for $ 1.05m. The property was completed in 2016 but I recently had to sell and it was sold for $965k. Does the loss have to stay in the company name or can it be set against personal income?

nope. its stuck there.
if the company is the trustee of a trust and held the property in trust for the benefit of the trust beneficiaries....its still stuck there.
bit of a bugger that. I presume that there was a good reason to acquire property in a company name, but it limits your options come time to sell said property.
sorry Tony. no good news for you today I am afraid

bc