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The commission will undergo its annual scheduled audit next week and environmentalists are hoping this will result in it losing the certification, which shows its products come from sustainable operations.
The audit is being conducted by Soil Association Woodmark, which itself will be audited at the same time by Accreditation Services International (ASI).
WA Conservation Council director Piers Verstegen said consumers were being duped.
"It's clear to everybody that these are not responsibly managed forests that are not sustainably harvested — we're talking about clearfelling of ancient forests, old growth forests that are habitat for threatened species," he said.
"This is not a sustainable management regime for these forests and shouldn't be given a green tick or any sort of certification.
"The Forest Products Commission have deliberately misrepresented the nature of their logging activities to the auditor in order to gain this certification.
"There's now an independent investigation of this forest certification process here in Western Australia, and we're confident that that will result in the certification being withdrawn from the Forest Products Commission."
Old growth forest not harvested: Commission
A Forest Products Commission spokeswoman told the ABC no old growth forest was harvested.
In a statement, the commission said claims that FPC's operations did not conform to the requirements of the standard would be "tested by the audit process".
"We are confident that out forest management practices represent a very high standard of sustainability and are independently reviewed and audited by the Department of Parks and Wildlife, Conservation Commission, the Environmental Protection Authority and two independent auditing companies," the statement said.
The Forest Stewardship Council (FSC), which sets the standards, said the ASI audit was routine.
But FSC Australia chief executive Adam Beaumont said it was important concerns were taken seriously.
"Forest managers who get a certificate need to be checked annually — every five years they've got to completely reapply," he said.
"ASI, who is effectively the auditor's auditor, their job is to also check certifying bodies or auditors every year, so this is part of that standard surveillance check.
"You cannot hold an FSC certificate unless you meet the FSC standard."
Clearfelling OK, Forest Stewardship Council says
The WA Forest Alliance has been running a campaign calling on the Forest Stewardship Council to refuse certification for "karri forest clear fells".
Mr Beaumont said the standard allowed for clearfelling.
"There's lots of different forest management techniques, the standard allows and provides for that," he said.
"What's important is that whatever the technique of harvesting that's involved, the forests are growing back, they're sustainable and the various aspects of wood forest management are adhered to.
"Ultimately the decision about whether a product carries an FSC logo is up to the auditor. Our job is to set the standard."
The WA Forest Alliance has highlighted the loss of a marri tree in Nelson forest near Bridgetown in the state's south-west, estimated to be 430 years old, and a karri tree believed to be about 275 years old.
Mr Beamuont said the cutting down of old trees was not an issue in itself, because the whole forest system needed to be taken into consideration.
"The FSC standard requires protection of multiple values across the landscape, not just old trees. Young trees become old trees as well," he said.
"It's important that we protect all the values and structures."
An FPC spokeswoman said larger trees in a harvest area were sometimes felled.