A handful of protesters outside the company's annual general meeting in Sydney on Thursday held signs accusing Woolworths of killing the Maugean skate, a prehistoric ray estimated to number between 40 to 120 individuals in the wild.
Inside, chairman Scott Perkins assured shareholders the board took the issue very seriously and urged them to vote down a motion to cease selling farmed salmon.
"Responsible sourcing of seafood is important to our business, and underpinned by our seafood sourcing policy, our policy requires all own branded seafood sold in Australia to be third party certified or independently verified as ecologically responsible," he said.
The remaining wild skates live exclusively in Tasmania's Macquarie Harbour, where salmon farming has been linked to problematic drops in available oxygen.
Campaigner Jess Coughlan said the clear consensus of scientists was that there would be catastrophic consequences unless urgent action is taken to remove the farms.
Oxygenation and captive breeding initiatives were showing promise, Mr Perkins said, arguing to wait until a review is completed after the federal election before making a decision on the future of the practice.
"It simply isn't the case, according to the advice we're getting, that the science is as black and white as you characterise it," he said
"We have no interest in precipitating an extinction event, so we look forward to being able to report back to you as soon as we can, as soon as these inquiries are completed."
The issues around salmon farming were complex and the livelihoods of people involved in the industry needed to be taken into account as well, Mr Perkins said.
Shareholders also questioned Woolworths' commitment to stamping out deforestation in its supply chain.
The big challenge in that respect was fresh beef, and the company would work closely with industry bodies to ensure a workable definition of no deforestation, Mr Perkins said.
He went on to reject allegations Woolworths misled customers by inflating prices on products before lowering them and calling it a discount.
Consumer watchdog the ACCC has launched legal action against Woolworths and Coles for the alleged tactics.
"Woolworths group is not perfect, and I'm sure we will learn things from some of these inquiries, but we remain firmly supportive of our teams and their conduct," he said.
"Specifically, we were disappointed with the ACCC's announcement to commence proceedings. And while we disagree with their assessment that the 'Prices Dropped' program was misleading, we are committed to working constructively with them."
The consumer watchdog is taking legal action against Woolworths over allegedly misleading discounts. (Con Chronis/AAP PHOTOS)
After receiving a first strike against its remuneration report last year, more than 95 per cent of shareholders voted in favour of executive pay, ensuring the board avoided a spill resolution.
It has been a damaging year for the reputation of Woolworths and Coles and a tricky first shareholder grilling for new chief executive Amanda Bardwell after her predecessor, Brad Banducci, resigned in February.
Woolworths has been in the firing line of 10 government inquiries, with Labor accusing the chains of buying land to stop competitors setting up shop and hiking prices for less product value.
The grocery chain revealed on Wednesday profits had taken a hit, with the company likely to make $1.48 billion in the December half, down from $1.6 billion a year earlier.
Woolworths' share price was down 1.8 per cent at midday.
