Penny Sharpe has voted against a motion, brought by the Greens in parliament, calling for the suspension of logging in nine state forests while investigations are carried out.
The motion was made after an audit by conservation groups found the Forestry Corporation had breached new greater glider search rules 188 times in just eight weeks.
The rules for pre-logging surveys were tightened in February after the corporation admitted it had been looking for nocturnal gliders during the day, when the animals would have been asleep inside their hollows.
The new rules require night-time spotlight surveys that must begin within an hour of sunset, when gliders typically head out to feed.
Penny Sharpe called for the suspension of logging in nine state forests as part of an investigation. (Bianca De Marchi/AAP PHOTOS)
That increases the chance of them being spotted in their den trees, which must not be destroyed.
But the audit found almost 80 per cent - or 188 of 243 audited searches - were done at the wrong time, leaving den trees vulnerable to logging.
The EPA had the results of the audit for two weeks but has so far not responded other than to say it is investigating the matter. Meanwhile, logging has continued at some sites.
Late on Wednesday, Greens MP Sue Higginson urged the government to direct the EPA to issue stop-work orders on all alleged non-compliant logging operations, while investigations are completed.
But Ms Sharpe said the EPA was independent.
"It is absolutely inappropriate for me to be directing the EPA," the minister told the house.
"It's like having the police minister direct the police, which we accept they don't do."
But Ms Higginson said "the reality is the EPA is answerable to the parliament" and the government had a duty to step in and halt what she called extinction logging.
The motion was defeated 26 to six, with the government and the opposition both rejecting it.
Nationals MP Sarah Mitchell said the timber industry operates under a very clear set of rules that manage issues like threatened species.
"Let the EPA do their work. Let the timber industry continue to do their important work, and leave it to the processes that are already in place to deal with these matters."
The Forestry Corporation previously told AAP "it is always our intention to apply the rules" and has been working closely with the EPA since they came into effect.
"That has included sharing all search and survey data with the EPA over this time."
The corporation says it's reviewing the audit released by conservation groups, which include Wilderness Australia, the Nature Conservation Council of NSW, South East Forest Rescue and the National Parks Association of NSW.
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