The victim was not booked in to stay at the building but was believed to be a guest of one of the two other people in the room.
All three are believed to have been known to police.
Details surrounding the shooting were hazy but police said there was no concerns for public safety, nor any evidence of drugs being manufactured in the room.
Mysteriously, no neighbouring guests reported hearing gunshots.
Auckland City Police Sergeant Graeme Lindner said two men had been identified from CCTV footage in connection to the shooting but were yet to be found.
Likewise, a weapon was yet to be located.
All three people were believed to be known to police.
"Staff are still at the hospital waiting to speak to the lady who was shot, we still haven't been able to do that."
Mr Lindner said that the room -- which had not been confirmed as a hotel room or an apartment -- had been forensically examined.
The victim was not booked in to stay at the building but was believed to be a guest of one of the two other people in the room.
Lindner said six officers were working on the case -- four from the Criminal Investigation Branch and two from the intelligence unit.
A receptionist at Auckland Harbour Oaks said the building's management was assisting police with their inquiries. She said there was no extra security at the building after the shooting, but only guests with key cards could enter.
Following the shooting, Senior Sergeant Matt Knowsley addressed media and said police were alerted to the incident by the ambulance service about 10.15am.
Mr Knowsley said officers had established the identity of some "persons of interest" by reviewing CCTV footage which included movement in corridors and lifts.
It was understood they were Maori or Pacific Islanders.
At the scene yesterday, four ambulances and four police cars were outside the building, which is flanked by a liquor store and beauty parlour.
An officer carrying a Taser at the entrance to the hotel checked visitors' identification as they entered the building and an armed officer holding a bullet-proof vest was seen leaving the hotel.
Several hotel occupants watched from the balconies of the 392-room, high-rise hotel as media and police gathered at the entrance, while others going in and out knew little or nothing about what was going on.
One couple staying in the building said they didn't hear anything out of the ordinary -- but they were concerned about staying there with the shooter still on the loose.