"The alliance has questioned why they continue rolling out the PHO solution and investing in it to improve it, when it will not be a fully electronic solution to the hospital, will never be integrated into hospital systems, and if ultimately they intend to turn it off in favour of the regional choice," Dr Bowers said.
Last week, the Otago Daily Times reported concerns outlined in a newsletter to Otago GPs that Southern PHO's system was engendering a "false sense of security", because doctors assumed referrals reached hospital departments when they did not.
GPs got an email indicating the referral had been received, when it still had to be printed and sent to hospital.
Dr Bowers said the alliance, consisting of South Island DHBs, was developing a regional e-referral system that was already in place in Canterbury.
It would be introduced in Southern at the end of this year, or slightly later.
"The mandate is that there will be a single electronic referrals system across the South Island, and only one.
"The Southern PHO was made aware of the need to support a regional system in writing during 2011, and it was indicated that the Southern DHB supports a whole of South Island development," Dr Bowers said.
He was concerned the PHO's system might hinder the South Island system.
"We have also been informed that as their referrals are tightly integrated into their system that they may have difficulty ever turning it off," Dr Bowers said.
In response, Southern PHO chief executive Ian Macara said the PHO supported the DHBs' approach and would work with the alliance.
"We'll be working with the DHBs as required to provide a solution that's best for patient care."
He declined to comment further.
Last week, he said the PHO system was having "teething problems".
The contract was controversial last year because of the perceived conflict of interest of Prof Murray Tilyard, the PHO's clinical review committee chairman, who was also chief executive of Best Practice Advocacy Centre Inc, which was awarded the contract.
