They had closed in on Naden's suspected campsite following a tip and were approaching from a number of directions when the single shot rang out. Police did not return fire, although they believe Naden will go down fighting rather than surrender.
The wounded officer has since been released from hospital.
"Naden is armed and he is dangerous," said NSW Police Commissioner Andrew Scipione.
"If he was cornered I am sure that he would be violent, so we are again repeating [to locals]: do not try and confront him, call triple-0, let the police do their job."
Scipione later told Sky News he was confident Naden would be found.
But Scipione conceded that Naden was a master bushman who knew the country, knew how to evade police, and could survive in conditions that would kill most others.
Late yesterday, with the police helicopter grounded by deteriorating weather, homicide Commander Mick Willing told ABC local radio time was working against police.
"It's difficult for the police officers up there searching, so I would assume it's difficult for him as well moving.
"We've had over 24 hours since that incident occurred so he could have moved some distance between that time and now."
Naden, a former abattoir worker, vanished after the body of Dubbo mother Kristy Scholes, 24, was found inside a house she had previously shared with Naden's cousin, Lateesha Nolan.
The three were members of an extended family.
Nolan was last seen in January 2005 when she dropped her two youngest children to join two older siblings at her grandmother's house, and left in her 1996 Ford Falcon after saying she would "only be a sec".
Her car was later found abandoned. There has been no sign of Nolan since.
In June 2005 the body of Scholes, 24, was found on the floor of her house. Her children, aged 3 and 4, had been left with their dead mother.
Naden disappeared soon afterwards, and a warrant for his arrest was issued, charging him with the murder.
Since then Naden has been on the run, sighted across vast areas of the state.
He is known to have spent some time at Dubbo's Western Plains Zoo, but is believed to have spent most of his time in rugged bush country ranging from Barrington Tops west of Taree to Tamworth in the north and Port Macquarie on the coast.
Searches have at various times focused on areas around Tamworth, Gunnedah, Armidale and Coonabarabran, and he was seen near Birdwood, west of Port Macquarie last February.
Earlier, searchers vainly scoured the Barrington Tops area when, wearing a mask and camouflage clothing, he woke a woman whose house he was burgling at Bellbrook, near Kempsey. This year a pig shooter found one of his hideouts in remote country.
The hunter told the Newcastle Herald that food was plentiful, with wallabies and kangaroos "so thick up there you almost trip over them".
The hunter added: "I would be very surprised if he does get caught."
