The multinational Bayer is expected to end global sales of endosulfan, replacing the toxic pesticide with safer alternatives.
But the Federal Government's pesticides authority continued to maintain the chemical was safe for use on a wide range of crops.
More than 60 countries have banned endosulfan. The chemical has been linked to reproductive and developmental damage in animals and humans, and residues have been detected in breast milk and placentas.
In October, the Stockholm Convention on Persistent Organic Pollutants, to which Australia is a signatory, will consider elevating endosulfan to the final stage of assessment, which if passed would trigger a gradual global ban.
Endosulfan is approved by the Australian Pesticides and Veterinary Medicines Authority for use on many crops, including tomatoes, citrus fruit and cotton.
Its possible use in a nut plantation at Noosa has still not been ruled out by an investigation into an outbreak of two-headed bass larvae at a neighbouring hatchery.
Bayer CropScience has appeared to pre-empt the Stockholm convention. In an email to the German-based Coalition Against Bayer Dangers it said: "We plan to stop the sale of the substance endosulfan by the end of 2010 in all the countries where it is still legally available."
The email, signed by Bayer CropScience's head of investor relations, Judith Nestmann, said endosulfan would be replaced by alternatives "with a significantly better risk profile".
Yesterday the pesticides authority's spokesman, Simon Cubit, said he was unaware of Bayer's decision, and reiterated the authority's stance that there were no human health issues associated with the use of endosulfan on Australian crops.
"We've got no scientific evidence that the way it is used in Australia is causing any problems," he said.
A spokeswoman for the National Toxics Network, Jo Immig, said: "Endosulfan is now banned in over 62 countries and it's high time Australia stopped trying to defend the indefensible."
A spokeswoman for the federal Agriculture Minister, Tony Burke, said that as the authority was an independent regulator, it would be inappropriate to comment.
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