A marine interest group has condemned giant cuttlefish research as scientifically flawed, but the scientist involved has defended it.

The Marine Life Society of South Australia said it doubted the accuracy of a study on the likely impact of shipping noise on the annual cuttlefish aggregation at the top of Spencer Gulf in South Australia.

The society said it was worried the report might be used to justify approval for the planned Port Bonython bulk commodities export facility near Point Lowly.

Society secretary Dan Monceaux questioned the research finding that the species, considered at risk by some, would not be affected by the sound of shipping.

"The conditions of the study don't match the conditions that the cuttlefish actually face in the wild," he said.

"The only way to really prove or disprove risk to the animals will be to make studies in the actual environment."

Research had budget and time constraints

But University of Adelaide researcher Professor Bronwyn Gillanders said her work did not need to completely replicate the marine conditions and budgetary and time restraints would have made that difficult.

"This was just the start to see if we could get an effect happening on giant Australian cuttlefish and at the moment it doesn't look like we can," she said, also indicating she hoped to make a further investigation of the issue.

"It's one of these classic studies when you find no effect [but] people will criticise it because they were wanting an effect."

A cuttlefish census this year found their numbers on the rise after several years of decline.

A year earlier, the census estimated a 27 per cent decline in the cuttlefish population, after an estimated 52 per cent fall in numbers between 2011 and 2012 and a 64 per cent decline between 2010 and 2011.

Each winter, the cuttlefish population aggregates at Point Lowly but numbers had gone into decline for about 15 years from a peak of about 200,000 in the late 1990s.

That trend had prompted the marine research efforts at a time when more industrial development was being proposed for the same region.