Clinical leader Dr Tim Kerruish said senior staff shared the concerns raised by their junior counterparts about the levels and proposed roster changes.
Chief operating officer Vivian Blake said she expected to meet staff representatives soon to better understand their concerns and "get to the bottom of it".
"If there is a safety issue in ED, we need to get on top of it, to ensure we are not compromising patient or staff safety," she said.
She had been working with staff to analyse the situation and ensure the department had the right "skill-mix" .
An April 1 letter to Mrs Blake signed by emergency department registrars and house surgeons, obtained by the Otago Daily Times shows they raised staffing concerns in December.
A New Zealand Resident Doctors Association (NZRDA) spokeswoman said those concerns related to night cover.
Only one registrar and one house surgeon were on duty between 1am and 7am during the week and midnight and 7am at weekends.
The doctors gave the example of a night in October, when the number of patients in the department at one time peaked at 35 and 41 patients were seen by the night shift doctor team during its shift.
In their letter, the doctors said they were grateful for progress but disappointed that it had taken more than three months for any potential plans to be presented.
Because of this, any recruitment to "ultimately solve the problem" would be even further delayed.
They took issue with what has been proposed, describing the planned night shift roster as one which would carry a "very high risk of fatigue which could lead to poor decision making".
They also say that having fewer registrars working during the day would "only lead to a redistribution of busy periods to later in the day", compounding night shift pressure and safety, particularly on weekends.
The doctors want an interim solution, with an expiry date and a "clear long-term strategy" to replace it.
They also raise the issue of difficulty in filling empty shifts at the hospital due to "non-competitive rates of pay" offered in comparison with surrounding hospitals.
They ask that the resident medical officers' unit pay these shifts at competitive rates which they said were $150 an hour or more.
Any solution, whether immediate, medium or long term had to be adequately resourced for it to work, the letter said.
Patient safety and compliance with the target, which requires 95% of patients to remain in the department for no longer than six hours, would not be "secured" without that.
Extra nursing staffing, introduced last year after nurses raised safety concerns, is still in place.
The NZRDA said it supported the registrars in their concerns and believed their interim solution was appropriate.
Mrs Blake, responding to recent comments by Dr Kerruish about his lack of confidence staying times would have improved by July, said she did not share his view.
There would be a number of opportunities for improvements before then.
She and intensivist Mike Hunter, who have been leading the "6 Hours - It Matters!" project which is taking a whole-of-systems approach to the issues were being told of improvements which could be made "almost on a daily basis".
It was a matter of staff "really coming on board" and understanding that it was a systems issue and a bed block issue and that there were a number of barriers to getting more timely care for ED patients.
Improving access to CT scanning was an example of something which had been identified as something which could make a difference.
The hospital has been under pressure to improve its ED staying times as it has been languishing near the bottom of national tables with only about 70% of patient stays meeting the target time.
