Responding to a highly critical National Health Board review of Dunedin Hospital systems, Dr Perez said doctors devised improvement schemes only to be turned away for lack of funds.
Although not blaming hospital managers for the resulting "impasse", structural change and stronger leadership was needed to find "feasible and affordable" solutions.
Funding woes accounted for "half" the hospital's woes, with the remainder being poor structures and lack of leadership.
In Saturday's Otago Daily Times, Southern DHB member Richard Thomson labelled the report a "little unfair" for not acknowledging the DHB's funding woes.
Dr Perez said managers were under "tremendous pressure" from Wellington to keep a tight rein on spending.
He agreed Dunedin and Southland hospitals operated as if there were still two DHBs, and the planning needed to provide healthcare across the whole region had been absent.
Such planning must be long-term as well as short and medium-term, and take into account the projected growth of Central Otago and the part played by Dunstan Hospital.
Such planning work had to be properly funded, he said. Talk of "regionalisation" of services for Otago and Southland was a "fancy concept" that even doctors did not understand fully at present.
Dunedin doctors had shown unwillingness to travel between hospitals - such reluctance was understandable but change could be negotiated.
"Doctors are going to have to change their work patterns," he said.
The super-size DHB should be presented to staff as an exciting opportunity to come up with clever ways to make it work.
Strong leadership was needed to counter "defensive" and "even aggressive" behaviour from those protecting their patch or specialty.
A medical oncologist, Dr Perez said it would make sense to have an Invercargill-based oncologist. In Dunedin there were seven.
Dr Perez said there was a feeling at Southland Hospital that Invercargill did not have its fair share of the Southern DHB health workforce.
Requiring travel, and basing more staff in Invercargill, could affect recruitment of senior medical staff.
It was difficult enough attracting senior medical staff to a city the size of Dunedin, and he believed that was why "disruptive" behaviour identified by the National Health Board report had been not been dealt with properly.
"Dunedin does find difficulty in attracting senior medical staff .
"People are reluctant to maybe work on people to the point where they leave or get sacked because it is hard to fill the gaps. There has been more tolerance for people acting... in a silo fashion rather than the best interests of the institution or the region."
