There are two major issues in the farming of Southern bluefin tuna (SBT): first, the catch of wild juveniles from a seriously depleted stock; second the confining in cages of the carnivorous species that has evolved to swim rapidly for thousands of kilometres.

SBT is overfished, subject to overfishing according to the Commonwealth’s own assessment [1].
Moreover SBT is listed as critically endangered by IUCN [2] because the stock has been depleted to less than 5 of the original.
Yet 5,239 tonnes of juvenile SBT were caught in Australian waters in 2007-2008, almost all destined for cages in South Australian waters.
If the long-terms survival of SBT is the goal then this level of catch must be brought into question.
Mortality can be assumed to be proceeded by suffering and it is this suffering associated with the process of death that makes mortality in caged fish an issue [3],[4].
In the article cited mortality of SBT in near-shore pens was at 10% over 3 to 6 months.
This could be considered as unacceptable from a welfare perspective, as well as being economically costly. The fact that mortality was reduced to more acceptable level of 5.5% in the offshore cages suggests that all SBT fattening cages should be moved offshore.

[1]Woodhams et al 2011: Fisheries status reports, at: http://www.daff.gov.au/abares/publications_remote_content/publication_series/fishery_status_report?sq_content_src=%2BdXJsPWh0dHAlM0ElMkYlMkYxNDMuMTg4LjE3LjIwJTJGYW5yZGwlMkZEQUZGU2VydmljZSUyRmRpc3BsYXkucGhwJTNGZmlkJTNEcGRfZmlzaHN0YXR1czIwMTA5YWJmZjAwMTAxXzExYS54bWwmYWxsPTE%3D
[2]IUCN, at: http://www.iucnredlist.org/search
[3]Ellis, T. et al, 2012. Mortality and fish welfare, Fish Physiol Biochem, 38: 189-199.
[4]Compassion in World Farming, 2009. Briefing: The welfare of farmed fish, at: http://www.ciwf.org.uk/includes/documents/cm_docs/2009/f/farmed_fish_briefing_aug2009.pdf